From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From zagahulik at gmail.com Sat Oct 15 03:30:55 2016 From: zagahulik at gmail.com (Boris Lahmadulin) Date: Sat, 15 Oct 2016 13:30:55 +0600 Subject: [Rtk-users] using >1 video cards Message-ID: Hello. I work with high resolution projections (32 mp) and reconstuction takes some longstanding time. At the same time there are two video cards in my computer, but uses only one. I wonder if i can use two video cards to reduce reconstruction time. What i tried to do in short: - execute this script on newest rtk revisiion for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) echo "!$i" p="_" grep -vE "(cuCtxSetCurrent)" $i > $i$p mv $i$p $i done i.e. remove all lines where happens setting of video card context - in rtkfdk.cxx by using posix threads create two threads, where i set contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) correspondingly and wait for signals; - in main thread for each working thread it created separated graphs, with reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] /= 2; origin+= ), fdk. - then fdk pointers put to shared data, so working threads can use them. After all signal is emmited and fdk->update() is called at working threads - since job is done, i copy two resulted subvolumes to one and save. it works and reconstuction time is reduced for about 1.5 times! However, if i run it a lot of times, finally it crashes with img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) ) Dimension: Dimension: 0x30x3 Index: Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] Size: Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, ] img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) Dimension: ] img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 ) Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] Dimension: 0x3 Index: [0, 0, 0] Size: [0x3e8, 0x29a, 0x1bc] ] ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line ExceptionObject caught with arg->fdk->Update() in file 242 rtkfdk.cxx line 242 itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError (0x7f45d048a100) 0x7f45d85a9ee0) Location: "unknown" Location: "unknown" File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/Core/Common/src/itkDataObject.cxx Line: 393 Description: Requested region is (at least partially) outside the largest possible region. 393 Description: Requested region is (at least partially) outside the largest possible region. It seems that itk classes are not reenterable, Is there way to fix it ? Or is there another way to make several video cards using for reconstuction in parallel ? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Sat Oct 15 05:12:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Sat, 15 Oct 2016 09:12:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> > Dear Sir\Madam, > > I am unable to do 1024x1024x1024 reconstruction using RTK > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of the > same. > > I am using the following items given below. > > 1. RTK - RTK version 1.3 > 2. ITK - ITK version 4.7 > 3. Visual Studio 2013 win 64-bit console application > 4. GeForce GTX TITAN X GPU. > 5. CUDA 7. > 6. CMake version 3.4.3. > 7. Windows 7 64-bit OS. > > Please provide the solution of this and let me know if any > other clarification is required. > > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > Bangalore - India. ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:27:32 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:27:32 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> References: <20161015091204.d79495bd@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, There is no screenshot so I'm guessing that the problem is a CUDA memory error. If you use the command line tool rtkfdk, you should first make sure that you use the --lowmem option to stream the projection images. If it is no sufficient, you can split your volume using the --divisions. The corresponding C++ code can be found in rtkfdk.cxx. Is Panacea Medical using RTK? We are happy to advertise the use of RTK on our case studies webpage . Simon On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < zahidhasan.a at panaceamedical.com> wrote: > > > Dear Sir\Madam, > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > the > > same. > > > > I am using the following items given below. > > > > 1. RTK - RTK version 1.3 > > 2. ITK - ITK version 4.7 > > 3. Visual Studio 2013 win 64-bit console application > > 4. GeForce GTX TITAN X GPU. > > 5. CUDA 7. > > 6. CMake version 3.4.3. > > 7. Windows 7 64-bit OS. > > > > Please provide the solution of this and let me know if any > > other clarification is required. > > > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > http://www.panaceamedical.com > > Bangalore - India. > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________ > ________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Oct 17 01:41:38 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 17 Oct 2016 07:41:38 +0200 Subject: [Rtk-users] using >1 video cards In-Reply-To: References: Message-ID: Hi, Interesting! I have never worked on that so... good luck! I have no idea why you get this error, maybe one of the filter is not threadsafe? But in my experience, ITK filters can be used like this. Maybe there is one issue in our CUDA framework which has never been tested in such a manner. I think you don't have to do your grep but replace the line m_DeviceIdx = itk::CudaGetMaxFlopsDev(); with the device of your choice in utilities/ITKCudaCommon/src/itkCudaContextManager.cxx. All the other cuCtxSetCurrent depend on that choice. What I would have done is changed this via an (optional) env variable and run rtkfdk twice to create each subvolume, each with a different thread. Good luck and keep us posted if you have a working solution. Simon On Sat, Oct 15, 2016 at 9:30 AM, Boris Lahmadulin wrote: > Hello. I work with high resolution projections (32 mp) and reconstuction > takes some longstanding time. At the same time there are two video cards in > my computer, but uses only one. I wonder if i can use two video cards to > reduce reconstruction time. > What i tried to do in short: > > - execute this script on newest rtk revisiion > for ($i in $(grep -nrl "cuCtxSetCurrent" utilities/ITKCudaCommon/*)) > echo "!$i" > p="_" > grep -vE "(cuCtxSetCurrent)" $i > $i$p > mv $i$p $i > done > i.e. remove all lines where happens setting of video card context > > - in rtkfdk.cxx by using posix threads create two threads, where i set > contexts through cuCtxSetCurrent(0) and cuCtxSetCurrentset(1) > correspondingly and wait for signals; > - in main thread for each working thread it created separated graphs, with > reader, ddf, pssf, constant (which is splitted by two, i.e. dimension[1] > /= 2; origin+= ), fdk. > - then fdk pointers put to shared data, so working threads can use them. > After all signal is emmited and fdk->update() is called at working threads > - since job is done, i copy two resulted subvolumes to one and save. > > it works and reconstuction time is reduced for about 1.5 times! However, > if i run it a lot of times, finally it crashes with > > img->GetRequestedRegion() = [ img->GetRequestedRegion() = [ > ImageRegionImageRegion ( (0x7f45f02293600x7f45f0229360) > ) > Dimension: Dimension: 0x30x3 > Index: > Index: [[00, , 0x14d0x14d, , 0xcf0xcf]] > Size: > Size: [[0x3e8, 0x14f, 0x3e8, 0x1]0x14f, > ] > img->GetLargestPossibleRegion() = [ 0x1ImageRegion (]0x7f45f0229328) > > Dimension: ] > img->GetLargestPossibleRegion() = [ ImageRegion (0x30x7f45f0229328 > ) > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > Dimension: 0x3 > Index: [0, 0, 0] > Size: [0x3e8, 0x29a, 0x1bc] > ] > ExceptionObject caught with arg->fdk->Update() in file rtkfdk.cxx line > ExceptionObject caught with arg->fdk->Update() in file 242 > rtkfdk.cxx line 242 > > > itk::InvalidRequestedRegionError (itk::InvalidRequestedRegionError > (0x7f45d048a100) > 0x7f45d85a9ee0) > Location: "unknown" > Location: "unknown" > File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: File: /home/koza/thirdparty/InsightToolkit-4.8.0/Modules/ > Core/Common/src/itkDataObject.cxx > Line: 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > 393 > Description: Requested region is (at least partially) outside the largest > possible region. > > > It seems that itk classes are not reenterable, Is there way to fix it ? Or > is there another way to make several video cards using for reconstuction in > parallel ? > > Thanks. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Mon Oct 17 08:27:04 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Mon, 17 Oct 2016 12:27:04 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Dear Simon Rit, Please find the screen shot in the attachment. Thanks & Regards Zahid Hasan Ansari Senior Design Engineer Mobile No. +91-9738379729 Panacea Medical Technologies Pvt. Ltd. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com Bangalore - India. ----- Original Message ----- From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > There is no screenshot so I'm guessing that the problem is a CUDA memory > error. If you use the command line tool rtkfdk, you should first make sure > that you use the --lowmem option to stream the projection images. If it is > no sufficient, you can split your volume using the --divisions. The > corresponding C++ code can be found in rtkfdk.cxx. > Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > our case studies webpage . > Simon > > On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > zahidhasan.a at panaceamedical.com> wrote: > > > > > > Dear Sir\Madam, > > > > > > I am unable to do 1024x1024x1024 reconstruction using RTK > > > CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > > the > > > same. > > > > > > I am using the following items given below. > > > > > > 1. RTK - RTK version 1.3 > > > 2. ITK - ITK version 4.7 > > > 3. Visual Studio 2013 win 64-bit console application > > > 4. GeForce GTX TITAN X GPU. > > > 5. CUDA 7. > > > 6. CMake version 3.4.3. > > > 7. Windows 7 64-bit OS. > > > > > > Please provide the solution of this and let me know if > any > > > other clarification is required. > > > > > > > > > > > > Thanks & Regards > > > > > > Zahid Hasan Ansari > > > Senior Design Engineer > > > Mobile No. +91-9738379729 > > > > > > Panacea Medical Technologies Pvt. Ltd. > > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, > > > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > > Malur - 563130. Kolar District. INDIA. > > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > > > http://www.panaceamedical.com > > > Bangalore - India. > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > > 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > ____________________________________________________________ > > ________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: RTK_Error.png Type: image/png Size: 42191 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Mon Oct 17 08:53:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Mon, 17 Oct 2016 14:53:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> References: <20161017122704.4410344e@PMT-SER-2.panaceamedical.com> Message-ID: <2154c2da-3a3a-7451-bddc-267da5ad9b97@creatis.insa-lyon.fr> Dear Zahid, Without some more information, it's unlikely that we find the source of the problem. Here are a few things you can do to help us (and therefore yourself): - try version 1.3.0 of RTK: there have been considerable changes in the Cuda forward and back projection filters since v1.2.0, so your problem might disappear just by upgrading to the new version - create a small example that reproduces your problem. You can, for example, simulate a geometry, simulate projections of a shepp logan phantom, and reconstruct from these projections (take a look at http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an example). And send us the script - OR send us your geometry file and the header of your projections file (no need to send the projection data itself, we'll create a zero-filled stack of projections), and the command line that crashes Best regards, Cyril On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > Dear Simon Rit, > > Please find the screen shot in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > Senior Design Engineer > Mobile No. +91-9738379729 > > Panacea Medical Technologies Pvt. Ltd. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : http://www.panaceamedical.com > Bangalore - India. > > > > > ----- Original Message ----- > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> There is no screenshot so I'm guessing that the problem is a CUDA memory >> error. If you use the command line tool rtkfdk, you should first make sure >> that you use the --lowmem option to stream the projection images. If it is >> no sufficient, you can split your volume using the --divisions. The >> corresponding C++ code can be found in rtkfdk.cxx. >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >> our case studies webpage . >> Simon >> >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >> zahidhasan.a at panaceamedical.com> wrote: >> >>>> Dear Sir\Madam, >>>> >>>> I am unable to do 1024x1024x1024 reconstruction using RTK >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>> the >>>> same. >>>> >>>> I am using the following items given below. >>>> >>>> 1. RTK - RTK version 1.3 >>>> 2. ITK - ITK version 4.7 >>>> 3. Visual Studio 2013 win 64-bit console application >>>> 4. GeForce GTX TITAN X GPU. >>>> 5. CUDA 7. >>>> 6. CMake version 3.4.3. >>>> 7. Windows 7 64-bit OS. >>>> >>>> Please provide the solution of this and let me know if >> any >>>> other clarification is required. >>>> >>>> >>>> >>>> Thanks & Regards >>>> >>>> Zahid Hasan Ansari >>>> Senior Design Engineer >>>> Mobile No. +91-9738379729 >>>> >>>> Panacea Medical Technologies Pvt. Ltd. >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>> Bangalore - India. >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>> Malur - 563130. Kolar District. INDIA. >>> >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> ____________________________________________________________ >>> ________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >>> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From zahidhasan.a at panaceamedical.com Wed Oct 19 09:18:57 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Wed, 19 Oct 2016 13:18:57 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Dear Cyril Mory, I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. Please find the attachment of the geometry file of our projections. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > Without some more information, it's unlikely that we find the source of > the problem. Here are a few things you can do to help us (and therefore > yourself): > - try version 1.3.0 of RTK: there have been considerable changes in the > Cuda forward and back projection filters since v1.2.0, so your problem > might disappear just by upgrading to the new version > - create a small example that reproduces your problem. You can, for > example, simulate a geometry, simulate projections of a shepp logan > phantom, and reconstruct from these projections (take a look at > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > example). And send us the script > - OR send us your geometry file and the header of your projections file > (no need to send the projection data itself, we'll create a zero-filled > stack of projections), and the command line that crashes > > Best regards, > Cyril > > On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > > Dear Simon Rit, > > > > Please find the screen shot in the attachment. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > Senior Design Engineer > > Mobile No. +91-9738379729 > > > > Panacea Medical Technologies Pvt. Ltd. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > http://www.panaceamedical.com > > Bangalore - India. > > > > > > > > > > ----- Original Message ----- > > From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > > Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> There is no screenshot so I'm guessing that the problem is a CUDA memory > >> error. If you use the command line tool rtkfdk, you should first make > sure > >> that you use the --lowmem option to stream the projection images. If it > is > >> no sufficient, you can split your volume using the --divisions. The > >> corresponding C++ code can be found in rtkfdk.cxx. > >> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on > >> our case studies webpage > . > >> Simon > >> > >> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >> zahidhasan.a at panaceamedical.com> wrote: > >> > >>>> Dear Sir\Madam, > >>>> > >>>> I am unable to do 1024x1024x1024 reconstruction using > RTK > >>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>> the > >>>> same. > >>>> > >>>> I am using the following items given below. > >>>> > >>>> 1. RTK - RTK version 1.3 > >>>> 2. ITK - ITK version 4.7 > >>>> 3. Visual Studio 2013 win 64-bit console application > >>>> 4. GeForce GTX TITAN X GPU. > >>>> 5. CUDA 7. > >>>> 6. CMake version 3.4.3. > >>>> 7. Windows 7 64-bit OS. > >>>> > >>>> Please provide the solution of this and let me know if > >> any > >>>> other clarification is required. > >>>> > >>>> > >>>> > >>>> Thanks & Regards > >>>> > >>>> Zahid Hasan Ansari > >>>> Senior Design Engineer > >>>> Mobile No. +91-9738379729 > >>>> > >>>> Panacea Medical Technologies Pvt. Ltd. > >>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>> Bangalore - India. > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > >>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >>> Malur - 563130. Kolar District. INDIA. > >>> > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> ____________________________________________________________ > >>> ________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- A non-text attachment was scrubbed... Name: geo.xml Type: text/xml Size: 126449 bytes Desc: not available URL: From cyril.mory at creatis.insa-lyon.fr Wed Oct 19 10:14:35 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 19 Oct 2016 16:14:35 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> References: <20161019131857.e3dbc200@PMT-SER-2.panaceamedical.com> Message-ID: <649935b5-42dd-3c28-e48d-da323278b9fa@creatis.insa-lyon.fr> Hello Zahid, We will need the header of your projections file, too (It is best if you have all your projections as a single .mhd and a single .raw file, so it should be 3-D image, and you send only the .mhd file). Regards, Cyril On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > Dear Cyril Mory, > > > I have only used RTK version 1.3.0. but in the error message it is showing RTK version 1.2.0. > > Please find the attachment of the geometry file of our projections. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> Without some more information, it's unlikely that we find the source of >> the problem. Here are a few things you can do to help us (and therefore >> yourself): >> - try version 1.3.0 of RTK: there have been considerable changes in the >> Cuda forward and back projection filters since v1.2.0, so your problem >> might disappear just by upgrading to the new version >> - create a small example that reproduces your problem. You can, for >> example, simulate a geometry, simulate projections of a shepp logan >> phantom, and reconstruct from these projections (take a look at >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >> example). And send us the script >> - OR send us your geometry file and the header of your projections file >> (no need to send the projection data itself, we'll create a zero-filled >> stack of projections), and the command line that crashes >> >> Best regards, >> Cyril >> >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>> Dear Simon Rit, >>> >>> Please find the screen shot in the attachment. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> Senior Design Engineer >>> Mobile No. +91-9738379729 >>> >>> Panacea Medical Technologies Pvt. Ltd. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >> http://www.panaceamedical.com >>> Bangalore - India. >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >> saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> There is no screenshot so I'm guessing that the problem is a CUDA memory >>>> error. If you use the command line tool rtkfdk, you should first make >> sure >>>> that you use the --lowmem option to stream the projection images. If it >> is >>>> no sufficient, you can split your volume using the --divisions. The >>>> corresponding C++ code can be found in rtkfdk.cxx. >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK on >>>> our case studies webpage >> . >>>> Simon >>>> >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>> zahidhasan.a at panaceamedical.com> wrote: >>>> >>>>>> Dear Sir\Madam, >>>>>> >>>>>> I am unable to do 1024x1024x1024 reconstruction using >> RTK >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>> the >>>>>> same. >>>>>> >>>>>> I am using the following items given below. >>>>>> >>>>>> 1. RTK - RTK version 1.3 >>>>>> 2. ITK - ITK version 4.7 >>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>> 4. GeForce GTX TITAN X GPU. >>>>>> 5. CUDA 7. >>>>>> 6. CMake version 3.4.3. >>>>>> 7. Windows 7 64-bit OS. >>>>>> >>>>>> Please provide the solution of this and let me know if >>>> any >>>>>> other clarification is required. >>>>>> >>>>>> >>>>>> >>>>>> Thanks & Regards >>>>>> >>>>>> Zahid Hasan Ansari >>>>>> Senior Design Engineer >>>>>> Mobile No. +91-9738379729 >>>>>> >>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>> Bangalore - India. >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>>> Malur - 563130. Kolar District. INDIA. >>>>> >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> ____________________________________________________________ >>>>> ________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >>> _______________________________________________ >>> Rtk-users mailing list >>> Rtk-users at public.kitware.com >>> http://public.kitware.com/mailman/listinfo/rtk-users >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > From s.cimen at sheffield.ac.uk Fri Oct 21 08:48:46 2016 From: s.cimen at sheffield.ac.uk (Serkan Cimen) Date: Fri, 21 Oct 2016 13:48:46 +0100 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry Message-ID: Hi, I am trying to understand the RTK geometry, but I am a bit confused. I wrote the following: #include "rtkThreeDCircularProjectionGeometry.h" typedef rtk::ThreeDCircularProjectionGeometry GeometryType; int main(int argc, char *argv[]) { int argOffset = 1; double gantryAngle = atof(argv[argOffset++]); double outOfPlaneAngle = atof(argv[argOffset++]); double inPlaneAngle = atof(argv[argOffset++]); double sid = atof(argv[argOffset++]); double sdd = atof(argv[argOffset++]); GeometryType::Pointer rtkGeo = GeometryType::New(); rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); std::cout << rtkGeo->GetSourcePosition(0) << std::endl; return EXIT_SUCCESS; } With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but I get [0,0,400,1]. The reason for my expectation is this sentence from geometry description file: "With all parameters set to 0, the detector is normal to the z direction of the fixed coordinate system". I drew a sketch (please see attached) of what I understood from this sentence, and was wondering if I am correct? It looks like I am missing something trivial, but couldn't figure out what. Many thanks in advance. Kind regards, Serkan -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Geometry.png Type: image/png Size: 53721 bytes Desc: not available URL: From simon.rit at creatis.insa-lyon.fr Fri Oct 21 09:28:14 2016 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 21 Oct 2016 15:28:14 +0200 Subject: [Rtk-users] Source position - ThreeDCircularProjectionGeometry In-Reply-To: References: Message-ID: Hi, Sorry, I guess the geometry is not perfectly explained. The source should be in the positive Z if you have a positive sdd, see "6.2 Source position" section of the geometry document . I enclose a drawing to help you visualize this (which will make it to the doxygen doc when I find the time to put everything there). Simon On Fri, Oct 21, 2016 at 2:48 PM, Serkan Cimen wrote: > Hi, > > I am trying to understand the RTK geometry, but I am a bit confused. I > wrote the following: > > #include "rtkThreeDCircularProjectionGeometry.h" > typedef rtk::ThreeDCircularProjectionGeometry GeometryType; > int main(int argc, char *argv[]) > { > int argOffset = 1; > double gantryAngle = atof(argv[argOffset++]); > double outOfPlaneAngle = atof(argv[argOffset++]); > double inPlaneAngle = atof(argv[argOffset++]); > double sid = atof(argv[argOffset++]); > double sdd = atof(argv[argOffset++]); > > GeometryType::Pointer rtkGeo = GeometryType::New(); > rtkGeo->AddProjection(sid, sdd, gantryAngle, 0.0, 0.0, > outOfPlaneAngle, inPlaneAngle, 0.0, 0.0); > std::cout << rtkGeo->GetSourcePosition(0) << std::endl; > > return EXIT_SUCCESS; > } > > With inputs 0 0 0 400 1000, I expect to get the source at [0,0,-400 1] but > I get [0,0,400,1]. The reason for my expectation is this sentence from > geometry description file: > "With all parameters set to 0, the detector is normal to the z direction > of the fixed coordinate system". I drew a sketch (please see attached) of > what I understood from this sentence, and was wondering if I am correct? > > It looks like I am missing something trivial, but couldn't figure out > what. Many thanks in advance. > > Kind regards, > Serkan > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: geometry.pdf Type: application/pdf Size: 30868 bytes Desc: not available URL: From zahidhasan.a at panaceamedical.com Tue Oct 25 03:22:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 07:22:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Dear Sir, The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? Or can you provide us the PC configuration to solve the issue? Let me know if any other clarification is required. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Hello Zahid, > > We will need the header of your projections file, too (It is best if you > have all your projections as a single .mhd and a single .raw file, so it > should be 3-D image, and you send only the .mhd file). > > Regards, > Cyril > > On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > > Dear Cyril Mory, > > > > > > I have only used RTK version 1.3.0. but in the error > message it is showing RTK version 1.2.0. > > > > Please find the attachment of the geometry file of our > projections. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Dear Zahid, > >> > >> Without some more information, it's unlikely that we find the source of > >> the problem. Here are a few things you can do to help us (and therefore > >> yourself): > >> - try version 1.3.0 of RTK: there have been considerable changes in the > >> Cuda forward and back projection filters since v1.2.0, so your problem > >> might disappear just by upgrading to the new version > >> - create a small example that reproduces your problem. You can, for > >> example, simulate a geometry, simulate projections of a shepp logan > >> phantom, and reconstruct from these projections (take a look at > >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >> example). And send us the script > >> - OR send us your geometry file and the header of your projections file > >> (no need to send the projection data itself, we'll create a zero-filled > >> stack of projections), and the command line that crashes > >> > >> Best regards, > >> Cyril > >> > >> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>> Dear Simon Rit, > >>> > >>> Please find the screen shot in the attachment. > >>> > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> Senior Design Engineer > >>> Mobile No. +91-9738379729 > >>> > >>> Panacea Medical Technologies Pvt. Ltd. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >> http://www.panaceamedical.com > >>> Bangalore - India. > >>> > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], > >> saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> There is no screenshot so I'm guessing that the problem is a CUDA > memory > >>>> error. If you use the command line tool rtkfdk, you should first make > >> sure > >>>> that you use the --lowmem option to stream the projection images. If it > >> is > >>>> no sufficient, you can split your volume using the --divisions. The > >>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK > on > >>>> our case studies webpage > >> . > >>>> Simon > >>>> > >>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>> zahidhasan.a at panaceamedical.com> wrote: > >>>> > >>>>>> Dear Sir\Madam, > >>>>>> > >>>>>> I am unable to do 1024x1024x1024 reconstruction > using > >> RTK > >>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of > >>>>> the > >>>>>> same. > >>>>>> > >>>>>> I am using the following items given below. > >>>>>> > >>>>>> 1. RTK - RTK version 1.3 > >>>>>> 2. ITK - ITK version 4.7 > >>>>>> 3. Visual Studio 2013 win 64-bit console application > >>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>> 5. CUDA 7. > >>>>>> 6. CMake version 3.4.3. > >>>>>> 7. Windows 7 64-bit OS. > >>>>>> > >>>>>> Please provide the solution of this and let me know > if > >>>> any > >>>>>> other clarification is required. > >>>>>> > >>>>>> > >>>>>> > >>>>>> Thanks & Regards > >>>>>> > >>>>>> Zahid Hasan Ansari > >>>>>> Senior Design Engineer > >>>>>> Mobile No. +91-9738379729 > >>>>>> > >>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, > >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>> http://www.panaceamedical.com > >>>>>> Bangalore - India. > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>>> Malur - 563130. Kolar District. INDIA. > >>>>> > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> ____________________________________________________________ > >>>>> ________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>> > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >>> > >>> > >>> _______________________________________________ > >>> Rtk-users mailing list > >>> Rtk-users at public.kitware.com > >>> http://public.kitware.com/mailman/listinfo/rtk-users > >> > > > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. From cyril.mory at creatis.insa-lyon.fr Tue Oct 25 03:48:31 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 25 Oct 2016 09:48:31 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> References: <20161025072209.be09c97c@PMT-SER-2.panaceamedical.com> Message-ID: <4bd0639e-3671-fdfc-19c3-7f315e5a95ff@creatis.insa-lyon.fr> Dear Zahid, We do not need the projections file, at least not for a first stage of error tracking. We only need the header. Try the following command line: rtkprojections -p . -r yourProjectionsFileName -o proj.mhd It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is what we need, and it is a very light text file. The "proj.raw" contains the pixel values, but at the moment we do not need them. We will create our own proj.raw file, filled with zeros, which should be enough to track down the error you encounter. Looking forward to receiving your file, Cyril On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > Dear Sir, > > The single raw file of the projections is 1.4 GB and we are not able to send this big file to you. Can you please suggest other alternatives for this? > > Or can you provide us the PC configuration to solve the issue? > > Let me know if any other clarification is required. > > > Thanks & Regards > > Zahid Hasan Ansari > > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Hello Zahid, >> >> We will need the header of your projections file, too (It is best if you >> have all your projections as a single .mhd and a single .raw file, so it >> should be 3-D image, and you send only the .mhd file). >> >> Regards, >> Cyril >> >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>> Dear Cyril Mory, >>> >>> >>> I have only used RTK version 1.3.0. but in the error >> message it is showing RTK version 1.2.0. >>> Please find the attachment of the geometry file of our >> projections. >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Dear Zahid, >>>> >>>> Without some more information, it's unlikely that we find the source of >>>> the problem. Here are a few things you can do to help us (and therefore >>>> yourself): >>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>> might disappear just by upgrading to the new version >>>> - create a small example that reproduces your problem. You can, for >>>> example, simulate a geometry, simulate projections of a shepp logan >>>> phantom, and reconstruct from these projections (take a look at >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>> example). And send us the script >>>> - OR send us your geometry file and the header of your projections file >>>> (no need to send the projection data itself, we'll create a zero-filled >>>> stack of projections), and the command line that crashes >>>> >>>> Best regards, >>>> Cyril >>>> >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>> Dear Simon Rit, >>>>> >>>>> Please find the screen shot in the attachment. >>>>> >>>>> >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> Senior Design Engineer >>>>> Mobile No. +91-9738379729 >>>>> >>>>> Panacea Medical Technologies Pvt. Ltd. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>> http://www.panaceamedical.com >>>>> Bangalore - India. >>>>> >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>> Cc: rtk-users at public.kitware.com [mailto:rtk-users at public.kitware.com], >>>> saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >> memory >>>>>> error. If you use the command line tool rtkfdk, you should first make >>>> sure >>>>>> that you use the --lowmem option to stream the projection images. If it >>>> is >>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of RTK >> on >>>>>> our case studies webpage >>>> . >>>>>> Simon >>>>>> >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>> >>>>>>>> Dear Sir\Madam, >>>>>>>> >>>>>>>> I am unable to do 1024x1024x1024 reconstruction >> using >>>> RTK >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot of >>>>>>> the >>>>>>>> same. >>>>>>>> >>>>>>>> I am using the following items given below. >>>>>>>> >>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>> 3. Visual Studio 2013 win 64-bit console application >>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>> 5. CUDA 7. >>>>>>>> 6. CMake version 3.4.3. >>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>> >>>>>>>> Please provide the solution of this and let me know >> if >>>>>> any >>>>>>>> other clarification is required. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Thanks & Regards >>>>>>>> >>>>>>>> Zahid Hasan Ansari >>>>>>>> Senior Design Engineer >>>>>>>> Mobile No. +91-9738379729 >>>>>>>> >>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>> http://www.panaceamedical.com >>>>>>>> Bangalore - India. >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> ____________________________________________________________ >>>>>>> ________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Rtk-users mailing list >>>>> Rtk-users at public.kitware.com >>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >> >> > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. > > > From zahidhasan.a at panaceamedical.com Tue Oct 25 07:13:09 2016 From: zahidhasan.a at panaceamedical.com (Zahid Hasan Ansari) Date: Tue, 25 Oct 2016 11:13:09 +0000 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error Message-ID: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Dear Sir, Please find the Header file in the attachment. Thanks & Regards Zahid Hasan Ansari ----- Original Message ----- From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > Dear Zahid, > > We do not need the projections file, at least not for a first stage of > error tracking. We only need the header. > Try the following command line: > > rtkprojections -p . -r yourProjectionsFileName -o proj.mhd > > It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is > what we need, and it is a very light text file. The "proj.raw" contains > the pixel values, but at the moment we do not need them. We will create > our own proj.raw file, filled with zeros, which should be enough to > track down the error you encounter. > > Looking forward to receiving your file, > Cyril > > On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: > > Dear Sir, > > > > The single raw file of the projections is 1.4 GB and we are not > able to send this big file to you. Can you please suggest other alternatives > for this? > > > > Or can you provide us the PC configuration to solve the issue? > > > > Let me know if any other clarification is required. > > > > > > Thanks & Regards > > > > Zahid Hasan Ansari > > > > > > > > ----- Original Message ----- > > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit > [mailto:simon.rit at creatis.insa-lyon.fr] > > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > > > > >> Hello Zahid, > >> > >> We will need the header of your projections file, too (It is best if you > >> have all your projections as a single .mhd and a single .raw file, so it > >> should be 3-D image, and you send only the .mhd file). > >> > >> Regards, > >> Cyril > >> > >> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: > >>> Dear Cyril Mory, > >>> > >>> > >>> I have only used RTK version 1.3.0. but in the error > >> message it is showing RTK version 1.2.0. > >>> Please find the attachment of the geometry file of our > >> projections. > >>> > >>> Thanks & Regards > >>> > >>> Zahid Hasan Ansari > >>> > >>> > >>> > >>> ----- Original Message ----- > >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon > Rit > >> [mailto:simon.rit at creatis.insa-lyon.fr] > >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>> > >>> > >>>> Dear Zahid, > >>>> > >>>> Without some more information, it's unlikely that we find the source of > >>>> the problem. Here are a few things you can do to help us (and therefore > >>>> yourself): > >>>> - try version 1.3.0 of RTK: there have been considerable changes in the > >>>> Cuda forward and back projection filters since v1.2.0, so your problem > >>>> might disappear just by upgrading to the new version > >>>> - create a small example that reproduces your problem. You can, for > >>>> example, simulate a geometry, simulate projections of a shepp logan > >>>> phantom, and reconstruct from these projections (take a look at > >>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an > >>>> example). And send us the script > >>>> - OR send us your geometry file and the header of your projections file > >>>> (no need to send the projection data itself, we'll create a zero-filled > >>>> stack of projections), and the command line that crashes > >>>> > >>>> Best regards, > >>>> Cyril > >>>> > >>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: > >>>>> Dear Simon Rit, > >>>>> > >>>>> Please find the screen shot in the attachment. > >>>>> > >>>>> > >>>>> Thanks & Regards > >>>>> > >>>>> Zahid Hasan Ansari > >>>>> Senior Design Engineer > >>>>> Mobile No. +91-9738379729 > >>>>> > >>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>> http://www.panaceamedical.com > >>>>> Bangalore - India. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] > >>>>> Cc: rtk-users at public.kitware.com > [mailto:rtk-users at public.kitware.com], > >>>> saimahesh.m at panaceamedical.com > >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > >>>>> > >>>>> > >>>>>> Dear Zahid, > >>>>>> There is no screenshot so I'm guessing that the problem is a CUDA > >> memory > >>>>>> error. If you use the command line tool rtkfdk, you should first make > >>>> sure > >>>>>> that you use the --lowmem option to stream the projection images. If > it > >>>> is > >>>>>> no sufficient, you can split your volume using the --divisions. The > >>>>>> corresponding C++ code can be found in rtkfdk.cxx. > >>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of > RTK > >> on > >>>>>> our case studies webpage > >>>> . > >>>>>> Simon > >>>>>> > >>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < > >>>>>> zahidhasan.a at panaceamedical.com> wrote: > >>>>>> > >>>>>>>> Dear Sir\Madam, > >>>>>>>> > >>>>>>>> I am unable to do 1024x1024x1024 reconstruction > >> using > >>>> RTK > >>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot > of > >>>>>>> the > >>>>>>>> same. > >>>>>>>> > >>>>>>>> I am using the following items given below. > >>>>>>>> > >>>>>>>> 1. RTK - RTK version 1.3 > >>>>>>>> 2. ITK - ITK version 4.7 > >>>>>>>> 3. Visual Studio 2013 win 64-bit console > application > >>>>>>>> 4. GeForce GTX TITAN X GPU. > >>>>>>>> 5. CUDA 7. > >>>>>>>> 6. CMake version 3.4.3. > >>>>>>>> 7. Windows 7 64-bit OS. > >>>>>>>> > >>>>>>>> Please provide the solution of this and let me > know > >> if > >>>>>> any > >>>>>>>> other clarification is required. > >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> Thanks & Regards > >>>>>>>> > >>>>>>>> Zahid Hasan Ansari > >>>>>>>> Senior Design Engineer > >>>>>>>> Mobile No. +91-9738379729 > >>>>>>>> > >>>>>>>> Panacea Medical Technologies Pvt. Ltd. > >>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, > >>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : > >>>>>>>> http://www.panaceamedical.com > >>>>>>>> Bangalore - India. > >>>>>>> ________________________________________ > >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > >> Phase > >>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > >> Area, > >>>>>>> Malur - 563130. Kolar District. INDIA. > >>>>>>> > >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>>>> Fax : + 91 80 42428710 > >>>>>>> Url : http://www.panaceamedical.com > >>>>>>> ____________________________________________________________ > >>>>>>> ________________ > >>>>>>> PMT EMAIL DISCLAIMER: > >>>>>>> > >>>>>>> This email and any files transmitted with it are confidential and > >>>> intended > >>>>>>> solely for the use of the individual or entity to whom they are > >>>> addressed. > >>>>>>> If you have received this email in error please notify the system > >>>> manager. > >>>>>>> Please note that any views or opinions presented in this email are > >>>> solely > >>>>>>> those of the author and do not necessarily represent those of the > >>>> company. > >>>>>>> Finally, the recipient should check this email and any attachments > for > >>>> the > >>>>>>> presence of viruses. The company accepts no liability for any damage > >>>>>>> caused by any virus transmitted by this email. > >>>>>>> > >>>>>>> > >>>>>>> _______________________________________________ > >>>>>>> Rtk-users mailing list > >>>>>>> Rtk-users at public.kitware.com > >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>>>>>> > >>>>> ________________________________________ > >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area > Phase > >> 1, > >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial > Area, > >>>> Malur - 563130. Kolar District. INDIA. > >>>>> Tel : +91 80 4242 8700 / 2845 4785 > >>>>> Fax : + 91 80 42428710 > >>>>> Url : http://www.panaceamedical.com > >>>>> > >> > ____________________________________________________________________________ > >>>>> PMT EMAIL DISCLAIMER: > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >> intended > >>>>> solely for the use of the individual or entity to whom they are > >> addressed. > >>>>> If you have received this email in error please notify the system > >> manager. > >>>>> Please note that any views or opinions presented in this email are > >> solely > >>>>> those of the author and do not necessarily represent those of the > >> company. > >>>>> Finally, the recipient should check this email and any attachments for > >> the > >>>>> presence of viruses. The company accepts no liability for any damage > >>>>> caused by any virus transmitted by this email. > >>>>> > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Rtk-users mailing list > >>>>> Rtk-users at public.kitware.com > >>>>> http://public.kitware.com/mailman/listinfo/rtk-users > >>> ________________________________________ > >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase > 1, > >> Whitefield, Bangalore - 560 066, Karnataka, INDIA > >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > >> Malur - 563130. Kolar District. INDIA. > >>> Tel : +91 80 4242 8700 / 2845 4785 > >>> Fax : + 91 80 42428710 > >>> Url : http://www.panaceamedical.com > >>> > >> > ____________________________________________________________________________ > >>> PMT EMAIL DISCLAIMER: > >>> > >>> This email and any files transmitted with it are confidential and > intended > >>> solely for the use of the individual or entity to whom they are > addressed. > >>> If you have received this email in error please notify the system > manager. > >>> Please note that any views or opinions presented in this email are > solely > >>> those of the author and do not necessarily represent those of the > company. > >>> Finally, the recipient should check this email and any attachments for > the > >>> presence of viruses. The company accepts no liability for any damage > >>> caused by any virus transmitted by this email. > >>> > >> > >> > > ________________________________________ > > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, > Whitefield, Bangalore - 560 066, Karnataka, INDIA > > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, > Malur - 563130. Kolar District. INDIA. > > > > Tel : +91 80 4242 8700 / 2845 4785 > > Fax : + 91 80 42428710 > > Url : http://www.panaceamedical.com > > > ____________________________________________________________________________ > > PMT EMAIL DISCLAIMER: > > > > This email and any files transmitted with it are confidential and intended > > solely for the use of the individual or entity to whom they are addressed. > > If you have received this email in error please notify the system manager. > > Please note that any views or opinions presented in this email are solely > > those of the author and do not necessarily represent those of the company. > > Finally, the recipient should check this email and any attachments for the > > presence of viruses. The company accepts no liability for any damage > > caused by any virus transmitted by this email. > > > > > > > > > ________________________________________ PANACEA MEDICAL TECHNOLOGIES PVT. LTD. Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. Tel : +91 80 4242 8700 / 2845 4785 Fax : + 91 80 42428710 Url : http://www.panaceamedical.com ____________________________________________________________________________ PMT EMAIL DISCLAIMER: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. Please note that any views or opinions presented in this email are solely those of the author and do not necessarily represent those of the company. Finally, the recipient should check this email and any attachments for the presence of viruses. The company accepts no liability for any damage caused by any virus transmitted by this email. -------------- next part -------------- ObjectType = Image NDims = 3 BinaryData = True BinaryDataByteOrderMSB = False CompressedData = False TransformMatrix = 1 0 0 0 1 0 0 0 1 Offset = -212.972 -212.972 -158.5 CenterOfRotation = 0 0 0 AnatomicalOrientation = RAI ElementSpacing = 0.296 0.296 0.296 DimSize = 1440 1440 349 ElementType = MET_USHORT ElementDataFile = Output.raw From cyril.mory at creatis.insa-lyon.fr Wed Oct 26 10:16:20 2016 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Wed, 26 Oct 2016 16:16:20 +0200 Subject: [Rtk-users] Reg: CBCT 1k reconstruction error In-Reply-To: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> References: <20161025111309.c74e1352@PMT-SER-2.panaceamedical.com> Message-ID: Dear Zahid, I was able to perform a reconstruction from your header and geometry file, using the following command lines: rtkprojectshepploganphantom -o simulatedprojections.mha -g geo.xml --phantomscale "128,128,128" --like Output.mhd rtkfdk -p . -r simulatedprojections.mha -g geo.xml -o fdk.mha --hardware cuda --dimension 1024 --spacing 0.25 --lowmem --divisions 4 The first computes projections through a Shepp & Logan phantom, with the same size, spacing, origin, etc... as your projections, using your geometry file geo.xml. The second line performs the FDK reconstruction. I had to use both the "--lowmem" and the "--divisions 4" since I have little GPU memory (3GB, on a Geforce GTX 780). "--lowmem" loads the projections into memory by subsets of 16. "--divisions 4" cuts the reconstructed volume into 4 parts, reconstructs them one by one, then assembles the results. Can you run the same commands and let us know whether you still encounter the crash you mentioned ? If it works, you can use your own projection data in the second command line instead of "simulatedprojections.mha". Best, Cyril On 10/25/2016 01:13 PM, Zahid Hasan Ansari wrote: > Dear Sir, > > Please find the Header file in the attachment. > > > Thanks & Regards > > Zahid Hasan Ansari > > > ----- Original Message ----- > From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] > Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com > Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error > > >> Dear Zahid, >> >> We do not need the projections file, at least not for a first stage of >> error tracking. We only need the header. >> Try the following command line: >> >> rtkprojections -p . -r yourProjectionsFileName -o proj.mhd >> >> It should write a "proj.mhd" and a "proj.raw". The "proj.mhd" file is >> what we need, and it is a very light text file. The "proj.raw" contains >> the pixel values, but at the moment we do not need them. We will create >> our own proj.raw file, filled with zeros, which should be enough to >> track down the error you encounter. >> >> Looking forward to receiving your file, >> Cyril >> >> On 10/25/2016 09:22 AM, Zahid Hasan Ansari wrote: >>> Dear Sir, >>> >>> The single raw file of the projections is 1.4 GB and we are not >> able to send this big file to you. Can you please suggest other alternatives >> for this? >>> Or can you provide us the PC configuration to solve the issue? >>> >>> Let me know if any other clarification is required. >>> >>> >>> Thanks & Regards >>> >>> Zahid Hasan Ansari >>> >>> >>> >>> ----- Original Message ----- >>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon Rit >> [mailto:simon.rit at creatis.insa-lyon.fr] >>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>> >>> >>>> Hello Zahid, >>>> >>>> We will need the header of your projections file, too (It is best if you >>>> have all your projections as a single .mhd and a single .raw file, so it >>>> should be 3-D image, and you send only the .mhd file). >>>> >>>> Regards, >>>> Cyril >>>> >>>> On 10/19/2016 03:18 PM, Zahid Hasan Ansari wrote: >>>>> Dear Cyril Mory, >>>>> >>>>> >>>>> I have only used RTK version 1.3.0. but in the error >>>> message it is showing RTK version 1.2.0. >>>>> Please find the attachment of the geometry file of our >>>> projections. >>>>> Thanks & Regards >>>>> >>>>> Zahid Hasan Ansari >>>>> >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] >>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com], Simon >> Rit >>>> [mailto:simon.rit at creatis.insa-lyon.fr] >>>>> Cc: rtk-users at public.kitware.com, saimahesh.m at panaceamedical.com >>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>> >>>>> >>>>>> Dear Zahid, >>>>>> >>>>>> Without some more information, it's unlikely that we find the source of >>>>>> the problem. Here are a few things you can do to help us (and therefore >>>>>> yourself): >>>>>> - try version 1.3.0 of RTK: there have been considerable changes in the >>>>>> Cuda forward and back projection filters since v1.2.0, so your problem >>>>>> might disappear just by upgrading to the new version >>>>>> - create a small example that reproduces your problem. You can, for >>>>>> example, simulate a geometry, simulate projections of a shepp logan >>>>>> phantom, and reconstruct from these projections (take a look at >>>>>> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK if you need an >>>>>> example). And send us the script >>>>>> - OR send us your geometry file and the header of your projections file >>>>>> (no need to send the projection data itself, we'll create a zero-filled >>>>>> stack of projections), and the command line that crashes >>>>>> >>>>>> Best regards, >>>>>> Cyril >>>>>> >>>>>> On 10/17/2016 02:27 PM, Zahid Hasan Ansari wrote: >>>>>>> Dear Simon Rit, >>>>>>> >>>>>>> Please find the screen shot in the attachment. >>>>>>> >>>>>>> >>>>>>> Thanks & Regards >>>>>>> >>>>>>> Zahid Hasan Ansari >>>>>>> Senior Design Engineer >>>>>>> Mobile No. +91-9738379729 >>>>>>> >>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>> http://www.panaceamedical.com >>>>>>> Bangalore - India. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr] >>>>>>> To: Zahid Hasan Ansari [mailto:zahidhasan.a at panaceamedical.com] >>>>>>> Cc: rtk-users at public.kitware.com >> [mailto:rtk-users at public.kitware.com], >>>>>> saimahesh.m at panaceamedical.com >>>>>>> Subject: Re: [Rtk-users] Reg: CBCT 1k reconstruction error >>>>>>> >>>>>>> >>>>>>>> Dear Zahid, >>>>>>>> There is no screenshot so I'm guessing that the problem is a CUDA >>>> memory >>>>>>>> error. If you use the command line tool rtkfdk, you should first make >>>>>> sure >>>>>>>> that you use the --lowmem option to stream the projection images. If >> it >>>>>> is >>>>>>>> no sufficient, you can split your volume using the --divisions. The >>>>>>>> corresponding C++ code can be found in rtkfdk.cxx. >>>>>>>> Is Panacea Medical using RTK? We are happy to advertise the use of >> RTK >>>> on >>>>>>>> our case studies webpage >>>>>> . >>>>>>>> Simon >>>>>>>> >>>>>>>> On Sat, Oct 15, 2016 at 11:12 AM, Zahid Hasan Ansari < >>>>>>>> zahidhasan.a at panaceamedical.com> wrote: >>>>>>>> >>>>>>>>>> Dear Sir\Madam, >>>>>>>>>> >>>>>>>>>> I am unable to do 1024x1024x1024 reconstruction >>>> using >>>>>> RTK >>>>>>>>>> CudaFDKConeBeamReconstructionFilter. Please check the screen shoot >> of >>>>>>>>> the >>>>>>>>>> same. >>>>>>>>>> >>>>>>>>>> I am using the following items given below. >>>>>>>>>> >>>>>>>>>> 1. RTK - RTK version 1.3 >>>>>>>>>> 2. ITK - ITK version 4.7 >>>>>>>>>> 3. Visual Studio 2013 win 64-bit console >> application >>>>>>>>>> 4. GeForce GTX TITAN X GPU. >>>>>>>>>> 5. CUDA 7. >>>>>>>>>> 6. CMake version 3.4.3. >>>>>>>>>> 7. Windows 7 64-bit OS. >>>>>>>>>> >>>>>>>>>> Please provide the solution of this and let me >> know >>>> if >>>>>>>> any >>>>>>>>>> other clarification is required. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Thanks & Regards >>>>>>>>>> >>>>>>>>>> Zahid Hasan Ansari >>>>>>>>>> Senior Design Engineer >>>>>>>>>> Mobile No. +91-9738379729 >>>>>>>>>> >>>>>>>>>> Panacea Medical Technologies Pvt. Ltd. >>>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, >>>>>>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 | Fax : + 91 42428710 | Url : >>>>>>>>>> http://www.panaceamedical.com >>>>>>>>>> Bangalore - India. >>>>>>>>> ________________________________________ >>>>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >>>> Phase >>>>>>>>> 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >>>> Area, >>>>>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>>>> >>>>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>>>> Fax : + 91 80 42428710 >>>>>>>>> Url : http://www.panaceamedical.com >>>>>>>>> ____________________________________________________________ >>>>>>>>> ________________ >>>>>>>>> PMT EMAIL DISCLAIMER: >>>>>>>>> >>>>>>>>> This email and any files transmitted with it are confidential and >>>>>> intended >>>>>>>>> solely for the use of the individual or entity to whom they are >>>>>> addressed. >>>>>>>>> If you have received this email in error please notify the system >>>>>> manager. >>>>>>>>> Please note that any views or opinions presented in this email are >>>>>> solely >>>>>>>>> those of the author and do not necessarily represent those of the >>>>>> company. >>>>>>>>> Finally, the recipient should check this email and any attachments >> for >>>>>> the >>>>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>>>> caused by any virus transmitted by this email. >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Rtk-users mailing list >>>>>>>>> Rtk-users at public.kitware.com >>>>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>>>> >>>>>>> ________________________________________ >>>>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area >> Phase >>>> 1, >>>>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial >> Area, >>>>>> Malur - 563130. Kolar District. INDIA. >>>>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>>>> Fax : + 91 80 42428710 >>>>>>> Url : http://www.panaceamedical.com >>>>>>> >> ____________________________________________________________________________ >>>>>>> PMT EMAIL DISCLAIMER: >>>>>>> >>>>>>> This email and any files transmitted with it are confidential and >>>> intended >>>>>>> solely for the use of the individual or entity to whom they are >>>> addressed. >>>>>>> If you have received this email in error please notify the system >>>> manager. >>>>>>> Please note that any views or opinions presented in this email are >>>> solely >>>>>>> those of the author and do not necessarily represent those of the >>>> company. >>>>>>> Finally, the recipient should check this email and any attachments for >>>> the >>>>>>> presence of viruses. The company accepts no liability for any damage >>>>>>> caused by any virus transmitted by this email. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> Rtk-users at public.kitware.com >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>> ________________________________________ >>>>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>>>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase >> 1, >>>> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>>>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >>>> Malur - 563130. Kolar District. INDIA. >>>>> Tel : +91 80 4242 8700 / 2845 4785 >>>>> Fax : + 91 80 42428710 >>>>> Url : http://www.panaceamedical.com >>>>> >> ____________________________________________________________________________ >>>>> PMT EMAIL DISCLAIMER: >>>>> >>>>> This email and any files transmitted with it are confidential and >> intended >>>>> solely for the use of the individual or entity to whom they are >> addressed. >>>>> If you have received this email in error please notify the system >> manager. >>>>> Please note that any views or opinions presented in this email are >> solely >>>>> those of the author and do not necessarily represent those of the >> company. >>>>> Finally, the recipient should check this email and any attachments for >> the >>>>> presence of viruses. The company accepts no liability for any damage >>>>> caused by any virus transmitted by this email. >>>>> >>>> >>> ________________________________________ >>> PANACEA MEDICAL TECHNOLOGIES PVT. LTD. >>> Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, >> Whitefield, Bangalore - 560 066, Karnataka, INDIA >>> Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, >> Malur - 563130. Kolar District. INDIA. >>> Tel : +91 80 4242 8700 / 2845 4785 >>> Fax : + 91 80 42428710 >>> Url : http://www.panaceamedical.com >>> >> ____________________________________________________________________________ >>> PMT EMAIL DISCLAIMER: >>> >>> This email and any files transmitted with it are confidential and intended >>> solely for the use of the individual or entity to whom they are addressed. >>> If you have received this email in error please notify the system manager. >>> Please note that any views or opinions presented in this email are solely >>> those of the author and do not necessarily represent those of the company. >>> Finally, the recipient should check this email and any attachments for the >>> presence of viruses. The company accepts no liability for any damage >>> caused by any virus transmitted by this email. >>> >>> >>> >> >> > > ________________________________________ > PANACEA MEDICAL TECHNOLOGIES PVT. LTD. > Head Office: Plot #119, GF, Envision Technology Center, EPIP Area Phase 1, Whitefield, Bangalore - 560 066, Karnataka, INDIA > Manufacturing Unit: Plot #87 A, Phase -II, Malur KIADB Industrial Area, Malur - 563130. Kolar District. INDIA. > > Tel : +91 80 4242 8700 / 2845 4785 > Fax : + 91 80 42428710 > Url : http://www.panaceamedical.com > ____________________________________________________________________________ > PMT EMAIL DISCLAIMER: > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are addressed. > If you have received this email in error please notify the system manager. > Please note that any views or opinions presented in this email are solely > those of the author and do not necessarily represent those of the company. > Finally, the recipient should check this email and any attachments for the > presence of viruses. The company accepts no liability for any damage > caused by any virus transmitted by this email. >