From guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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 guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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 guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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 guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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 guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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 guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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 guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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 guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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 guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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 guangming.zang at kaust.edu.sa Wed Sep 2 04:24:58 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Wed, 2 Sep 2015 11:24:58 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK Message-ID: Hi Simon, i was wondering how to call the rtkrabbit application in RTK?? it seems that there is no ggo file yet?? And if not available?? do you know how to use rtk to convert the dataset "rabbitct_512-v2.rctd" in RABBIT CT website to .mha or .mhd format?? Thanks very much in advance. Regards Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Sep 2 09:17:42 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 2 Sep 2015 15:17:42 +0200 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Hi, This is not an application, it's a library that must be linked to the rabbit CT application that is provided on the website. To be honest, this has been developed a long time ago and I haven't updated it in a long time (2012 according to the git log, I think the rabbit CT dataset has changed since). Apparently, the cmake option in RTK to compile it has been removed so this is currently a dead code. That would be very nice if you'd want to bring it back to life, we'd really appreciate it. Simon On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang wrote: > Hi Simon, > i was wondering how to call the rtkrabbit application > in > RTK?? > it seems that there is no ggo file yet?? > And if not available?? do you know how to use rtk to convert the dataset > "rabbitct_512-v2.rctd" in RABBIT CT website > to .mha or > .mhd format?? > > Thanks very much in advance. > Regards > Guangming > > *Guangming Zang (Alex)* > *King Abdullah University of Science and Technology(KAUST)* > *University of Chinese Academy of Sciences(UCAS)* > > > > > ------------------------------ > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From guangming.zang at kaust.edu.sa Fri Sep 4 07:07:25 2015 From: guangming.zang at kaust.edu.sa (Guangming Zang) Date: Fri, 4 Sep 2015 14:07:25 +0300 Subject: [Rtk-users] How to call rtkrabbitct application in RTK In-Reply-To: References: Message-ID: Ok, i see. Yes, maybe later i may try this data set and manage to add it on RTK. Thanks Guangming *Guangming Zang (Alex)* *King Abdullah University of Science and Technology(KAUST)* *University of Chinese Academy of Sciences(UCAS)* 2015-09-02 16:17 GMT+03:00 Simon Rit : > Hi, > This is not an application, it's a library that must be linked to the > rabbit CT application that is provided on the website. To be honest, this > has been developed a long time ago and I haven't updated it in a long time > (2012 according to the git log, I think the rabbit CT dataset has changed > since). Apparently, the cmake option in RTK to compile it has been removed > so this is currently a dead code. That would be very nice if you'd want to > bring it back to life, we'd really appreciate it. > Simon > > On Wed, Sep 2, 2015 at 10:24 AM, Guangming Zang < > guangming.zang at kaust.edu.sa> wrote: > >> Hi Simon, >> i was wondering how to call the rtkrabbit application >> in >> RTK?? >> it seems that there is no ggo file yet?? >> And if not available?? do you know how to use rtk to convert the dataset >> "rabbitct_512-v2.rctd" in RABBIT CT website >> to .mha or >> .mhd format?? >> >> Thanks very much in advance. >> Regards >> Guangming >> >> *Guangming Zang (Alex)* >> *King Abdullah University of Science and Technology(KAUST)* >> *University of Chinese Academy of Sciences(UCAS)* >> >> >> >> >> ------------------------------ >> This message and its contents, including attachments are intended solely >> for the original recipient. If you are not the intended recipient or have >> received this message in error, please notify me immediately and delete >> this message from your computer system. Any unauthorized use or >> distribution is prohibited. Please consider the environment before printing >> this email. > > > -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 4 07:37:37 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 4 Sep 2015 13:37:37 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= Message-ID: Dear RTK users, I'd like to remind you that we're organizing a training on Wednesday, Nov 18 2015 in Lyon (France) in collaboration with Kitware. See further details and information on the website http://formations.kitware.fr/browse/116 and don't hesitate to contact us if you want to know more. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From pconneely020186 at gmail.com Fri Sep 4 16:55:45 2015 From: pconneely020186 at gmail.com (peter conneely) Date: Fri, 4 Sep 2015 21:55:45 +0100 Subject: [Rtk-users] Convert mha to dcm Message-ID: Hi all, I wasdoes anyone know a way to convert an .mha volume into dcm images. I'm trying to load the reconstructed volume into the PlanUnc treatment planning software but it only accepts .dcm files. Thanks, Peter -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Sat Sep 5 05:26:58 2015 From: julien.jomier at kitware.com (Julien Jomier) Date: Sat, 5 Sep 2015 11:26:58 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: References: Message-ID: <55EAB562.40606@kitware.com> Hi Peter, You can use Slicer (www.slicer.org). Hope that helps, Julien On 04/09/2015 22:55, peter conneely wrote: > Hi all, > > I wasdoes anyone know a way to convert an .mha volume into dcm images. > I'm trying to load the reconstructed volume into the PlanUnc treatment > planning software but it only accepts .dcm files. > > Thanks, > Peter > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From g.landry at physik.uni-muenchen.de Sat Sep 5 05:31:03 2015 From: g.landry at physik.uni-muenchen.de (Guillaume Landry) Date: Sat, 5 Sep 2015 11:31:03 +0200 Subject: [Rtk-users] Convert mha to dcm In-Reply-To: <55EAB562.40606@kitware.com> References: <55EAB562.40606@kitware.com> Message-ID: <55EAB657.6010703@physik.uni-muenchen.de> Hi, If you need a command line tool, plastimatch works great as well. Regards Guillaume Dr. Guillaume Landry Ludwig Maximilians University (LMU) Munich Medical Physics Am Coulombwall 1 85748 Garching Tel:+49 (0) 89 289-14077 Fax:+49 (0) 89 289-14072 On 09/05/2015 11:26 AM, Julien Jomier wrote: > Hi Peter, > > You can use Slicer (www.slicer.org). > > Hope that helps, > Julien > > On 04/09/2015 22:55, peter conneely wrote: >> Hi all, >> >> I wasdoes anyone know a way to convert an .mha volume into dcm images. >> I'm trying to load the reconstructed volume into the PlanUnc treatment >> planning software but it only accepts .dcm files. >> >> Thanks, >> Peter >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at public.kitware.com >> http://public.kitware.com/mailman/listinfo/rtk-users >> > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Sep 7 03:41:20 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 7 Sep 2015 09:41:20 +0200 Subject: [Rtk-users] Pixel value and mha dcm conversion In-Reply-To: References: Message-ID: (Please use the mailing list) Hi, No, there is no post-processing option in RTK to rescale the reconstructed values but this is rather easy to do by adding an ITK filter such as RescaleIntensityImageFilter . There is no plan to add such options because I think the post-processing can be kept out of the command line tools. Simon On Sun, Sep 6, 2015 at 9:16 PM, peter conneely wrote: > > ---------- Forwarded message ---------- > From: peter conneely > Date: Sun, Sep 6, 2015 at 8:07 PM > Subject: Pixel value and mha dcm conversion > To: Rit Simon > > > Hi Simon, > > I have used RTK to reconstruct elekta data on Rando man ( i am also gong > to recon varian data in the future). When I compare to the reconstruction > performed by the elekta software I found that there is a significant > difference in HU e.g. .003 RTK ~500 Elekta. I found a thread discussing HU > and it mentions a value of 65536-1024. This factor appears to be why my > data is out. > Is there a way to reconstruct elekta data so that final image has HU > values are closer to -1000 1000? > > I tried to convert this mha file to dcm using slicer and plastimatch but > found a 0 pixel value image, is the problem above described the reason for > this incorrect conversion? > > I apologies if this trival but I have tried to figure it out but i'm at my > wits end. > > Thanks, > Peter > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Sep 25 09:49:02 2015 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 25 Sep 2015 15:49:02 +0200 Subject: [Rtk-users] =?utf-8?q?RTK_training=3A_early_bird_registration_sti?= =?utf-8?q?ll_possible_=E2=80=93_Register_now!!?= In-Reply-To: References: Message-ID: Dear all, We are now sure that the training will occur on Nov 18, we have a sufficient number of registrations. I'd like to invite other people that want to attend to register ASAP, even if you have one month left to enjoy the early bird registration. This will help us a lot to organize the logistic of the event! Thanks! Simon On Fri, Sep 4, 2015 at 1:37 PM, Simon Rit wrote: > Dear RTK users, > I'd like to remind you that we're organizing a training on Wednesday, Nov > 18 2015 in Lyon (France) in collaboration with Kitware. See further details > and information on the website http://formations.kitware.fr/browse/116 > and don't hesitate to contact us if you want to know more. > Simon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From joelbeaudry at gmail.com Fri Sep 25 23:32:30 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Fri, 25 Sep 2015 20:32:30 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example Message-ID: Hi RTK-users, I'm unable to reproduce the images from the 4DROOSTERReconstruction example. The 5 frames should show some differences pertaining to patient motion but the ones that I'm producing are identical, so no motion is visible. Has anyone been able to follow the example and the provided dataset to create a 4D image? Thanks, Joel -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Mon Sep 28 03:52:00 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 09:52:00 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: Message-ID: <5608F1A0.9010903@uclouvain.be> Hi Joel, I have just tried to reproduce the wiki example, and indeed, there are several mistakes in it. I am working on correcting them. I'll keep you posted. Cyril On 09/26/2015 05:32 AM, Joel Beaudry wrote: > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to > patient motion but the ones that I'm producing are identical, so no > motion is visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > 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 cyril.mory at uclouvain.be Mon Sep 28 07:48:54 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Mon, 28 Sep 2015 13:48:54 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <5608F1A0.9010903@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> Message-ID: <56092926.30609@uclouvain.be> Hi Joel, I have fixed the wiki example (command line parameters AND data). Can you restart it from scratch and let me know if you still have problems ? Roughly, the problems were the following: - the "mm_50.mha" motion mask file was not aligned with the CBCT coordinates - the regularization parameters (gamma space and gamma time) were way too high. The regularization with a high gamma-time caused frames to be identical, while it should only discourage variations I hope it works, now. If it doesn't work for you, please keep asking Cyril On 09/28/2015 09:52 AM, Cyril Mory wrote: > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to >> patient motion but the ones that I'm producing are identical, so no >> motion is visible. >> >> Has anyone been able to follow the example and the provided dataset >> to create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> 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 joelbeaudry at gmail.com Tue Sep 29 15:36:10 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Tue, 29 Sep 2015 12:36:10 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <56092926.30609@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: Hi Cyril, Works like a charm, thanks! I tried it on some other datasets and it seems to be working. I need to increase the resolution and play around with the parameters now. I haven't had time to test it too much, but I do get an error when attempting to reconstruct with different dimensions. I'm using Cuda, and haven't tried it with just cpu reconstruction yet. i.e.) --dimension 160 --spacing 2 -> works --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In AverageOutOfROIImageFilter: information of ROI image does not match input image" I'll be able to test some other things later and list more details. Thanks, Joel On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory wrote: > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). Can you > restart it from scratch and let me know if you still have problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were way too > high. The regularization with a high gamma-time caused frames to be > identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: > > Hi Joel, > > I have just tried to reproduce the wiki example, and indeed, there are > several mistakes in it. I am working on correcting them. I'll keep you > posted. > > Cyril > > > On 09/26/2015 05:32 AM, Joel Beaudry wrote: > > Hi RTK-users, > > I'm unable to reproduce the images from the 4DROOSTERReconstruction > example. The 5 frames should show some differences pertaining to patient > motion but the ones that I'm producing are identical, so no motion is > visible. > > Has anyone been able to follow the example and the provided dataset to > create a 4D image? > > Thanks, > Joel > > > _______________________________________________ > Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at uclouvain.be Wed Sep 30 03:33:10 2015 From: cyril.mory at uclouvain.be (Cyril Mory) Date: Wed, 30 Sep 2015 09:33:10 +0200 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> Message-ID: <560B9036.7060204@uclouvain.be> Hi Joel, Good to hear it's working now. The error you get is explained on the wiki in the small paragraph after the cuda command line : Note that the reconstructed volume in this example does not fully contain the attenuating object, causing hyper-attenuation artifacts on the borders of the result. To avoid these artifacts, reconstruct a larger volume (--dimension 256) should be fine. *Note that you will have to resize your motion mask as well, as 3D the motion mask is expected to have the same size, spacing and origin as the first 3 dimensions of the 4D output. * I guess I should take some time to fix that, and allow any motion mask, but until I do, you can resize your motion mask using the CLITK tools (http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. Cyril On 09/29/2015 09:36 PM, Joel Beaudry wrote: > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it > seems to be working. I need to increase the resolution and play around > with the parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, > and haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match > input image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > > Hi Joel, > > I have fixed the wiki example (command line parameters AND data). > Can you restart it from scratch and let me know if you still have > problems ? > > Roughly, the problems were the following: > - the "mm_50.mha" motion mask file was not aligned with the CBCT > coordinates > - the regularization parameters (gamma space and gamma time) were > way too high. The regularization with a high gamma-time caused > frames to be identical, while it should only discourage variations > > I hope it works, now. If it doesn't work for you, please keep asking > Cyril > > > On 09/28/2015 09:52 AM, Cyril Mory wrote: >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, >> there are several mistakes in it. I am working on correcting >> them. I'll keep you posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >>> Hi RTK-users, >>> >>> I'm unable to reproduce the images from the >>> 4DROOSTERReconstruction example. The 5 frames should show some >>> differences pertaining to patient motion but the ones that I'm >>> producing are identical, so no motion is visible. >>> >>> Has anyone been able to follow the example and the provided >>> dataset to create a 4D image? >>> >>> Thanks, >>> Joel >>> >>> >>> _______________________________________________ >>> 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 joelbeaudry at gmail.com Wed Sep 30 15:51:28 2015 From: joelbeaudry at gmail.com (Joel Beaudry) Date: Wed, 30 Sep 2015 12:51:28 -0700 Subject: [Rtk-users] 4DROOSTERReconstruction example In-Reply-To: <560B9036.7060204@uclouvain.be> References: <5608F1A0.9010903@uclouvain.be> <56092926.30609@uclouvain.be> <560B9036.7060204@uclouvain.be> Message-ID: Hi Cyril, The thing is I'm reconstructing a FDK image with dimensions 512 (0.88 spacing) and re-creating a mask off of that. So the motion mask should have the same dimensions, spacing, and origin as the intended 4D image since I'm using 4D rooster with --dimension 512 --spacing 0.88. Perhaps I'm creating my mask incorrectly? I'll try and fiddle with it a bit later and see why the mask I created for 160 (2), worked but not the case of 512 (0.88), and let you know what I find. Thanks again, Joel On Wed, Sep 30, 2015 at 12:33 AM, Cyril Mory wrote: > Hi Joel, > > Good to hear it's working now. > The error you get is explained on the wiki in the small paragraph after > the cuda command line : > > Note that the reconstructed volume in this example does not fully contain > the attenuating object, causing hyper-attenuation artifacts on the borders > of the result. To avoid these artifacts, reconstruct a larger volume > (--dimension 256) should be fine. *Note that you will have to resize your > motion mask as well, as 3D the motion mask is expected to have the same > size, spacing and origin as the first 3 dimensions of the 4D output. * > > I guess I should take some time to fix that, and allow any motion mask, > but until I do, you can resize your motion mask using the CLITK tools ( > http://www.creatis.insa-lyon.fr/rio/vv) or any method that suits you. > > Cyril > > > > On 09/29/2015 09:36 PM, Joel Beaudry wrote: > > Hi Cyril, > > Works like a charm, thanks! I tried it on some other datasets and it seems > to be working. I need to increase the resolution and play around with the > parameters now. > > I haven't had time to test it too much, but I do get an error when > attempting to reconstruct with different dimensions. I'm using Cuda, and > haven't tried it with just cpu reconstruction yet. > > i.e.) > --dimension 160 --spacing 2 -> works > --dimension 512,64,512 --spacing 0.88,2.5,0.88 --> throws "In > AverageOutOfROIImageFilter: information of ROI image does not match input > image" > > I'll be able to test some other things later and list more details. > > Thanks, > Joel > > > > On Mon, Sep 28, 2015 at 4:48 AM, Cyril Mory > wrote: > >> Hi Joel, >> >> I have fixed the wiki example (command line parameters AND data). Can you >> restart it from scratch and let me know if you still have problems ? >> >> Roughly, the problems were the following: >> - the "mm_50.mha" motion mask file was not aligned with the CBCT >> coordinates >> - the regularization parameters (gamma space and gamma time) were way too >> high. The regularization with a high gamma-time caused frames to be >> identical, while it should only discourage variations >> >> I hope it works, now. If it doesn't work for you, please keep asking >> Cyril >> >> >> On 09/28/2015 09:52 AM, Cyril Mory wrote: >> >> Hi Joel, >> >> I have just tried to reproduce the wiki example, and indeed, there are >> several mistakes in it. I am working on correcting them. I'll keep you >> posted. >> >> Cyril >> >> >> On 09/26/2015 05:32 AM, Joel Beaudry wrote: >> >> Hi RTK-users, >> >> I'm unable to reproduce the images from the 4DROOSTERReconstruction >> example. The 5 frames should show some differences pertaining to patient >> motion but the ones that I'm producing are identical, so no motion is >> visible. >> >> Has anyone been able to follow the example and the provided dataset to >> create a 4D image? >> >> Thanks, >> Joel >> >> >> _______________________________________________ >> Rtk-users mailing listRtk-users at public.kitware.comhttp://public.kitware.com/mailman/listinfo/rtk-users >> >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 16:44:37 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:44:37 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> Message-ID: <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park > wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 theday79 at gmail.com Wed Sep 30 16:59:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 16:59:06 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? Message-ID: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Hi all, This could be a silly question but, I'm just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I'm trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang -------------- next part -------------- An HTML attachment was scrubbed... URL: From theday79 at gmail.com Wed Sep 30 17:12:06 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 17:12:06 -0400 Subject: [Rtk-users] Generating signal data from Amsterdam Shroud In-Reply-To: <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> References: <02AABEED-A026-4581-B3BC-83E40720FBCD@mymail.vcu.edu> <00b101d0f24e$625fa2b0$271ee810$@gmail.com> <00c701d0f254$4af529a0$e0df7ce0$@gmail.com> <963E1047-7BC1-4C38-9E2A-9412F32421EE@mymail.vcu.edu> <003a01d0fbc0$d2c89e00$7859da00$@gmail.com> <9352809F-7403-4589-B7BE-FD7C0A9D4A69@mymail.vcu.edu> Message-ID: <005801d0fbc4$a9c70a60$fd551f20$@gmail.com> Hi Matt, Thank you so much for your help, again. Unfortunately, I?m using windows system (windows7 64 with VS 2013) and I guess this could be a challenging issue to me. Hi RTK users, Is there anyone who successfully compiled RTK with ?ITK + FFTW? in windows system? I?m just trying to use rtkextractshroudsignal and it seems to require FFTW library externally. When I tried to use FFTW 3.3.4, I?ve encountered link errors as shown below. Any help will be highly appreciated. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Wednesday, September 30, 2015 5:01 PM To: Yang K Park Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, I?m running on Ubuntu 14.04 LTS and used the distribution library (FFTW 3.3.3). If you?re running on a Debian-based linux system, you can also install the full development library set using the following command: sudo apt-get install libfftw3-3 libfftw3-dev. Then just make sure that these libraries are being used by rerunning CCMake. I?m not quite sure about the error being thrown in your build, but perhaps one of the main developers would be able to provide some more insight into the issue. Hope this helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 30, 2015, at 4:44 PM, Yang K Park > wrote: Hi Matt, Thank you so much for your advice. Recently I have revisited this project and tried to compile ITK with those options on as you suggested. I?ve tried to use the up-to-date version of FFTW (3.3.4), but it seems that it doesn?t work with RTK. There were some link errors like: rtkextractshroudsignal.obj : error LNK2019: unresolved external symbol __imp_fftw_execute referenced in function "protected: virtual void __cdecl itk::FFTWComplexToComplexFFTImageFilter,1> >::BeforeThreadedGenerateData(void)" (?BeforeThreadedGenerateData@? May I ask you which version of fftw you are successfully using in which system(Windows or Linux)? Thanks. Yang From: Matthew J. Riblett [mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 6:56 PM To: Yang K Park > Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Yang, One ITK requirement of the new RTK version is the inclusion of the Fast Fourier Transform components. This requires compilation with the ITK_USE_FFTWF and the ITK_USE_FFTWD options. I know, I didn?t compile that way initially, and it took a little bit of time to figure out. Hope that helps, ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:55 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matt, That sounds great! I really appreciate your advice. I?m now compiling itk-4.8 to use that feature since I?ve found my itk version is a bit obsolete (4.4). Thanks! Yang From: Matthew J. Riblett [ mailto:riblettmj at mymail.vcu.edu] Sent: Friday, September 18, 2015 4:31 PM To: Yang K Park < theday79 at gmail.com> Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Yang, Nice to hear from you! I have had some success since my initial posting ? in fact I?m currently working on a new method for accomplishing this task in certain challenging cases. The most recent version of RTK provides an update to the rtkextractshroudsignal application which provides a phase signal output when called using the ?-p? flag at runtime: rtkextractshroudsignal -i shroud.mhd -o raw_signal.txt -p phase_signal.txt --method LINEAR_BETWEEN_MINIMA >From what I?ve experienced, this generally provides a good signal [0,1) characterizing the respiratory phase using the default settings. Occasionally, I?ve run into issues where the default ?unsharpness? parameter needs to be adjusted to give a clear signal (by appending the --unsharp ## flag to the command). On more challenging shroud images ? notably, those with little detectable signal from background ? additional contrast-enhancement by pre-processing of the shroud has assisted in signal extraction. I hope that helps ? and please let me know how it works out for you. ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 On Sep 18, 2015, at 4:12 PM, Yang K Park < theday79 at gmail.com> wrote: Hi Matthew, Hello, I found you in the RTK-thread. Recently, I?ve encountered exactly same issue and it would be highly appreciated if you can share with me your updates on this issue. Thanks. Yang _______________________________________________ Yang-Kyun Park, Ph.D., DABR Assistant physicist & Instructor Department of Radiation Oncology Massachusetts General Hospital & Harvard Medical School 55 Fruit Street, Boston, MA 02114 Tel: +1-617-726-0186 Fax: +1-617-726-3603 From: Rtk-users [ mailto:rtk-users-bounces at public.kitware.com] On Behalf Of Joel Beaudry Sent: Tuesday, March 17, 2015 5:25 PM To: Matthew J. Riblett < riblettmj at mymail.vcu.edu> Cc: rtk-users at public.kitware.com Subject: Re: [Rtk-users] Generating signal data from Amsterdam Shroud Hi Matthew, I'm not sure of what was used in the Matlab script, but I've had good success with using a Hilbert function in python (scipy). I'm sure that Matlab has an equivalent function, and maybe that is what was used? Hope that helps, Joel On Wed, Mar 11, 2015 at 2:40 PM, Matthew J. Riblett < riblettmj at mymail.vcu.edu> wrote: Hello fellow RTK users, I was wondering if anyone has a straightforward method of going from the results of the rtkamsterdamshroud and rtkextractshroudsignal applications to a [0,1) phase signal for performing motion-compensated reconstruction. I?ve been following along with the MC-CBCT Reconstruction example ( http://wiki.openrtk.org/index.php/RTK/Examples/MCCBCTReconstruction), and there is an indication that Matlab is used to process the should signal prior to feeding it back into the reconstruction application, but there is no mention of how this is accomplished. I?m trying to implement this into an automated workflow and I?d love to know how this was accomplished. Thanks! ? Matt __ Matthew J. Riblett Virginia Commonwealth University Department of Radiation Oncology Medical Physics Graduate Program Office: Sanger Hall, Room B1-013 401 College Street | P.O. Box 980058 Richmond, Virginia 23298 VCU Email: riblettmj at vcu.edu MCV Office Phone: +1.804.628.4858 _______________________________________________ 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 WEICHENG.SHEN at leidos.com Wed Sep 30 17:32:49 2015 From: WEICHENG.SHEN at leidos.com (Shen, Weicheng) Date: Wed, 30 Sep 2015 21:32:49 +0000 Subject: [Rtk-users] Unknown CMake command "WRAP_GGO" Message-ID: <138BB7BB4B88944BBAF7E2E8FBCB55809C977025@EMP-EXMR104.corp.leidos.com> I am a new user of the RTK. The first thing I did is to build the RTK 1.1.0 using Microsoft Visual Studio 2013 on my Window 7 machine. After the RTK is successfully built, I attempted to build a sample application rtkMyApp following the instructions given at the rtktutorialapplication.cxx. rtkMyApp is really a copy of the rtktutorialapplication. Necessary changes are made according to the instructions in rtktutorialapplication.cxx However, when I use the CMake to build rtkMyApp, the following error appears in the "configure" phase: CMake Error at CMakeLists.txt:1 (WRAP_GGO): Unknown CMake command "WRAP_GGO". I couldn't figure out where WRAP_GGO is defined. Any help will be greatly appreciated. Thanks, Weicheng Shen, Ph.D. Lead Research Scientist | Leidos 4001 N. Fairfax Drive, Arlington, VA 22203 | Suite 700 O: (703) 907-2548 | Weicheng.shen at leidos.com [leidos_logo] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 15591 bytes Desc: image001.png URL: From theday79 at gmail.com Wed Sep 30 18:00:29 2015 From: theday79 at gmail.com (Yang K Park) Date: Wed, 30 Sep 2015 18:00:29 -0400 Subject: [Rtk-users] How to search for previous Q/A of RTK community? In-Reply-To: References: <004701d0fbc2$d89c1800$89d44800$@gmail.com> Message-ID: <006a01d0fbcb$6c182940$44487bc0$@gmail.com> Hi Joel, Even though I?m a windows user, I managed to carry out your method using Cygwin. My command was: wget -r -l1 --no-parent ?O rtkQA.txt http://public.kitware.com/pipermail/rtk-users/ Thank you very much for your help! Yang From: Joel Beaudry [mailto:joelbeaudry at gmail.com] Sent: Wednesday, September 30, 2015 5:19 PM To: Yang K Park Subject: Re: [Rtk-users] How to search for previous Q/A of RTK community? Hi Yang, "wget" can download all texts file from their respective month. Something like this below should work. wget -r -l1 --no-parent -A.txt http://public.kitware.com/pipermail/rtk-users/ Cheers, Joel On Wed, Sep 30, 2015 at 1:59 PM, Yang K Park > wrote: Hi all, This could be a silly question but, I?m just wondering if there is any way to download all the previous threads (as a text file) so that I can search through it using some key words. What I have found so far is this one: http://public.kitware.com/pipermail/rtk-users/ However, to find something I have to open each text file one by one. I?m trying to find a better way so that I can avoid bothering someone with questions that had been already answered before. Any suggestion would be highly appreciated. Thanks. Yang _______________________________________________ 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: