From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spollmann at robarts.ca Thu Aug 1 11:57:14 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 11:57:14 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Message-ID: Hey RTK Users, I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). Thanks again, Steve From spollmann at robarts.ca Thu Aug 1 16:53:50 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Thu, 1 Aug 2013 16:53:50 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: Message-ID: <51FACADE.10909@robarts.ca> Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjections.jpg Type: image/jpeg Size: 99195 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RawProjectionsAfterRAMP.jpg Type: image/jpeg Size: 115817 bytes Desc: not available URL: From Cyril.Mory at philips.com Fri Aug 2 03:09:03 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Fri, 2 Aug 2013 07:09:03 +0000 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <51FACADE.10909@robarts.ca> References: <51FACADE.10909@robarts.ca> Message-ID: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From spollmann at robarts.ca Sun Aug 4 14:19:54 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:19:54 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:20:52 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:20:52 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, Message-ID: Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From spollmann at robarts.ca Sun Aug 4 14:22:06 2013 From: spollmann at robarts.ca (Steven Pollmann) Date: Sun, 4 Aug 2013 14:22:06 -0400 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca>, <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com>, , Message-ID: Grrr.... e-mail program is auto-correcting! rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd Steve ________________________________________ From: Steven Pollmann Sent: August 4, 2013 2:20 PM To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just a quick correction... The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd Steve ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] Sent: August 4, 2013 2:19 PM To: MORY, CYRIL; rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hello, I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: https://app.box.com/s/bgh5a2i3grxi6lkltrj2 In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) :) Anyhow, thanks for looking at this data. Steven ________________________________________ From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] Sent: August 2, 2013 3:09 AM To: rtk-users at openrtk.org Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Hi Steve, The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann Envoy? : jeudi 1 ao?t 2013 22:54 ? : rtk-users at openrtk.org Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. Just an update on this issue I am having. If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. Any suggestions from here? Thanks! Steve On 13-08-01 11:57 AM, Steven Pollmann wrote: > Hey RTK Users, > > I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan > of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). > > Thanks again, > Steve > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:53:40 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:53:40 +0200 Subject: [Rtk-users] Joseph back projection filter In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801335009461@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, I can't remember exactly, this backprojection filter is quite experimental and not used a lot. After a quick check at the code, it seems that I kept an image of the backprojection weights to accumulate them and divide by their sum. The size of this image is taken from the largest possible region. Since this filter has been written, the behavior of the Joseph forward projection filter has been given the possibility to be templated with functors. I think the backprojection filter should be rewritten to use that possibility. Simon On Wed, Jul 31, 2013 at 3:31 PM, MORY, CYRIL wrote: > Hi RTK users, > > > > I just ran into trouble with the Joseph back projection filter. It crashed > with the error ?Largest and buffered region must be similar?. The other back > projection filters do not seem to have the same limitation, so I use > VoxelBasedBackProjection and it works fine, but I?m curious why this check > has been introduced in the Joseph back projection filter. > > > > Regards, > > ========================================== > > Cyril Mory > > PhD student at Philips Medisys and CREATIS > > > > Groupement Hospitalier Est > > H?pital Cardiologique Louis Pradel > > Laboratoire CREATIS - B?t. B13 > > CNRS UMR5220, INSERM U1044, INSA-Lyon, Univ. Lyon 1 > > 28, Avenue du Doyen LEPINE > > 69677 Bron cedex FRANCE > > > > Office : +33 4 72 35 74 12 > > Cell : +33 6 69 46 73 79 > > > > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby notified > that any use, forwarding, dissemination, or reproduction of this message is > strictly prohibited and may be unlawful. If you are not the intended > recipient, please contact the sender by return e-mail and destroy all copies > of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From simon.rit at creatis.insa-lyon.fr Mon Aug 12 04:59:28 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 10:59:28 +0200 Subject: [Rtk-users] RTK cone beam angle In-Reply-To: References: Message-ID: Hi, Please use the mailing list to get quicker answers. The cone-beam angle is determined by the source to detector distance and the size of your projection images (number of pixels and spacing). You can look at this document for a detailed description: http://www.openrtk.org/Doxygen/geometry.pdf Simon On Thu, Aug 1, 2013 at 2:20 AM, Rajeev Samarage wrote: > Hi Simon, > > I am trying to use the very feature-full software that you guys have > developed - RTK. I am wondering where I could change the cone beam angle of > the source within the software? > > Kind regards, > Rajeev > > -- > > Rajeev Samarage | Doctoral Candidate > > Laboratory for Dynamic Imaging | Department of Mechanical and Aerospace > Engineering > MONASH UNIVERSITY | VIC | 3800 | AUSTRALIA > > T +61 3 9905 1927 | W http://ldi.monash.edu.au From simon.rit at creatis.insa-lyon.fr Mon Aug 12 09:39:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 12 Aug 2013 15:39:49 +0200 Subject: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. In-Reply-To: References: <51FACADE.10909@robarts.ca> <3B67D2F1029933428E0E93E2C2F18013350097B0@011-DB3MPN1-042.MGDPHG.emi.philips.com> Message-ID: Hi Steven, Thanks for sharing the dataset. I had a look and it seems that some of your pixels contain nan values. In this case, one pixel can contaminate all the others, especially since RTK uses a 3D FFT (for speed). To illustrate this, I have enclosed a vv snapshot of the mhd of projection 525. At location of the crosshair, i.e. pixel (924,679), the value is nan. Surprisingly, when I ran statistics on the file, I found like you that nan values did not contaminate min/max but it did contaminate the sum. Simon On Sun, Aug 4, 2013 at 8:22 PM, Steven Pollmann wrote: > Grrr.... > e-mail program is auto-correcting! > rubiks_MM_PROJ.mhd NOT rubies_MM_PROJ.mhd > > > Steve > > ________________________________________ > From: Steven Pollmann > Sent: August 4, 2013 2:20 PM > To: Steven Pollmann; MORY, CYRIL; rtk-users at openrtk.org > Subject: RE: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just a quick correction... > The Projection .mhd file is called rubies_MM_PROJ.mhd, not rubies_MM_PROJ.mhd > > Steve > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of Steven Pollmann [spollmann at robarts.ca] > Sent: August 4, 2013 2:19 PM > To: MORY, CYRIL; rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hello, > I have finally been able to upload the Rubiks projections to Box.com. It is about 2GB. This is the link: > https://app.box.com/s/bgh5a2i3grxi6lkltrj2 > > In that directory, I have included a geometry file for reconstruction, and 2 linux tcsh scripts that I use to perform just a ramp filter, or a full fdk reconstruction (ZZ_doRamp.tcsh, and ZZ_doFDKRecon.tcsh). The projections are 1024x680 floating point, but I have created a rubies_MM_Proj.mhd with the appropriate info. > I have been playing a little more with the data, and I think the issue is possibly related to the top and bottom of the projections where a collimator is partially visible (These areas do not correct well with bright- and dark-field images, as I think the collumator changes a little between acquisitions of the bright and dark fields, and the actual projections). If I blank (set to 0.0), say the first 50 and last 50 lines, the ramp filter does not get an NaN, and is ok. It seems the RAMP filtering function is not handling some data in these region well, possibly resulting in a divide by zero? > > I've been using this data set with RTK to test some corrections we'd like to do on the projection images...and, also, it is a pretty fun dataset to work with (4x4x4 Rubiks Cube!) > :) > Anyhow, thanks for looking at this data. > Steven > > ________________________________________ > From: rtk-users-bounces at openrtk.org [rtk-users-bounces at openrtk.org] On Behalf Of MORY, CYRIL [Cyril.Mory at philips.com] > Sent: August 2, 2013 3:09 AM > To: rtk-users at openrtk.org > Subject: Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Hi Steve, > > The problem seems to lie in the data indeed. Can you send a link to the dataset (using a Dropbox link, for example) ? > > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de Steven Pollmann > Envoy? : jeudi 1 ao?t 2013 22:54 > ? : rtk-users at openrtk.org > Objet : Re: [Rtk-users] Volume error with fdkrtk backprojecting Polynomial corrected logged Projection Images. > > Just an update on this issue I am having. > If I just use rtkbackprojections with --method CudaBackProjection, I get an output volume that looks ok (obviously blurry, as no filter was applied). So I target my efforts to look into the Ramp Filter. It seems that this is where the issue stems from. I have included 2 image screenshots. The first (RawProjections.jpg) is a slice of the sinogram of the polynomial corrected projection data I would like to backproject, and the second (RawProjectionsRAMP.jpg) is the same data, after the RAMP filter has been applied (using rtkramp). The black lines contain "NaN" > values, and for that particular projection image, the entire image is turned into NaN. So the backprojection obciously fails through those values. > I will do one more check to see if there are any erroneous pixels for the projections where the NaN occurs, but I am not confident that there should be any abnormal values. > > Any suggestions from here? > Thanks! > Steve > > > > On 13-08-01 11:57 AM, Steven Pollmann wrote: >> Hey RTK Users, >> >> I'm having an issue with rtkfdk output that I am trying to track down. I'm using logged projection images that have had a polynomial-based correction applied to them. Every voxel in the output 3D mhd file (float) has a floating point value of 7FFFFFFF which, I believe is the largest 32bit float representation. The input projection images look fine when I open them with VolView (having values ranging from -0.3(air) to 45.0 (metal screw)). The original non-corrected projections (having values ranging from -0.02(air) to 2.88(screw)) work with rtkfdk to produce a nice looking volume, so there is something I am missing. Using in-house software, this polynomial corrected projection data reconstructs on a CPU-based implementation fine, however both CPU and CUDA backprojections from rtkfdk will not produce a valid 3d Volume for me. If anyone has insight into what change in the projection data may cause this, that would be appreciated. The dataset isn't proprietary (it is a scan >> of a 4x4x4 Rubiks Cube), and so I can send files to some online storage, if needed. (It is around 2GB of projection data...). >> >> Thanks again, >> Steve >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > ________________________________ > The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- A non-text attachment was scrubbed... Name: steven.tiff Type: image/tiff Size: 280748 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rubiks_MM_PROJ525.mhd Type: application/octet-stream Size: 189 bytes Desc: not available URL: From emaddox at planet.nl Mon Aug 26 05:47:38 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 11:47:38 +0200 Subject: [Rtk-users] how can I get a good 3d image? Message-ID: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. From Cyril.Mory at philips.com Mon Aug 26 07:22:47 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:22:47 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. From simon.rit at creatis.insa-lyon.fr Mon Aug 26 07:33:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 13:33:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image? > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message. > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Cyril.Mory at philips.com Mon Aug 26 07:39:25 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Mon, 26 Aug 2013 11:39:25 +0000 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Oups. My bad, I didn't know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From emaddox at planet.nl Mon Aug 26 08:11:32 2013 From: emaddox at planet.nl (emaddox at planet.nl) Date: 26 Aug 2013 14:11:32 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> Message-ID: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Hi, Thanks for the fast feedback. Below the commands that do the job. I am not yet happy with the image quality compared to our normal reconstruction, but it is a start. Any suggestions how to improve continue? C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml --proj_iso_x=-21.63 --p roj_iso_y=-54.08 C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g geometry 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 --dimension=256,640,256 Kind regards, Erik Maddox. ----Original Message---- >From : Cyril.Mory at philips.com Date : 26/08/2013 13:39 To : simon.rit at creatis.insa-lyon.fr Cc : emaddox at planet.nl, rtk-users at openrtk.org Subject : RE: [Rtk-users] how can I get a good 3d image? Oups. My bad, I didn?t know that. Thanks for your correction. De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : lundi 26 ao?t 2013 13:33 ? : MORY, CYRIL Cc : emaddox at planet.nl; rtk-users at openrtk.org Objet : Re: [Rtk-users] how can I get a good 3d image? Hi, Just a correction on Cyril's comment: there is a conversion to attenuation with tif images, see http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html It assumes that the maximum possible value is I0. You can check the result with rtkprojections -p. -r .*.tif -o proj.mha I think that the problem is that you don't define the position of your rotation center with the --proj_iso_x and --proj_iso_y options in rtksimulatedgeometry. If you don't set those, the rotation center on the projection image is assumed to be the point of coordinate (0,0), i.e., the first pixel of the image with tif images. The two above-mentioned options allow to translate this point. Simon On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL wrote: Hi Erik, Judging from the projection image you sent, you seem to be missing a crucial step. The area around your water cylinder is white and the cylinder itself is black. This is the raw data you obtain from a scanner. It is (more or less) the power received by each pixel of the detector. Before you backproject this, you have to convert it to attenuations. Check out the Wikipedia page http://en.wikipedia.org/wiki/Tomographic_reconstruction. Currently your images represent I, and you have to extract p. Only then can you hope to get something coherent from an FDK reconstruction. Best regards, Cyril -----Message d'origine----- De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] De la part de emaddox at planet.nl Envoy? : lundi 26 ao?t 2013 11:48 ? : rtk-users at openrtk.org Objet : [Rtk-users] how can I get a good 3d image? Hi, I tried to reconstruct with RTK an example CT data set of a water phantom but so far no success. I carefully checked all hints on the website and looked to the examples which I could run on my system. My data is acquired in a cone beam CT system. My projections are tif images, 103 images each rotated by 1.98 degree steps. The images are 640 by 512 pixels. Distances: source to detector is 255 mm, source to centre object is 200 mm commands I used: rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o geometry.xml rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 (I tried --dimension with single slice and all slices (640)) my projections: http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) can someone tell me if I can (and how to) get a good reconstruction with RTK of this water phantom? Kind regards, Erik Maddox. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message. _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Mon Aug 26 08:32:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 26 Aug 2013 14:32:07 +0200 Subject: [Rtk-users] how can I get a good 3d image? In-Reply-To: <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> References: <2929032.613171377510458685.JavaMail.defaultUser@defaultHost> <3B67D2F1029933428E0E93E2C2F180133501B3AA@011-DB3MPN1-041.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F180133501B3E0@011-DB3MPN1-041.MGDPHG.emi.philips.com> <5238068.645491377519092678.JavaMail.defaultUser@defaultHost> Message-ID: Can you be more specific about "not happy"? I think the geometry is now correct although a cylinder is not the best way to check. What you can improve is the conversion to attenuation by having the flood field images (projection without object in the FOV, see Cyril's link for its use), pre-processing the projections to remove noise (there is a median filter in RTK but you have to add it in the code), windowing during filtering to remove noise (see --hann option), etc. But you'll have to play with your data to find the best combination. Simon On Mon, Aug 26, 2013 at 2:11 PM, emaddox at planet.nl wrote: > Hi, > > Thanks for the fast feedback. > > Below the commands that do the job. I am not yet happy with the image > quality > compared to our normal reconstruction, but it is a start. Any suggestions > how to improve > continue? > > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtksimulatedgeometry.e > xe -n 103 -a 201.96 --sdd 255 --sid 200 -o geometry1.xml > --proj_iso_x=-21.63 --p > roj_iso_y=-54.08 > > C:\Users\erik\Software\RTK\RTK-tst>..\RTK-bin\bin\Release\rtkfdk.exe -g > geometry > 1.xml -p water -r .*.tif -o water.mha --spacing=0.169 > --dimension=256,640,256 > > Kind regards, > Erik Maddox. > > ----Original Message---- > From : Cyril.Mory at philips.com > Date : 26/08/2013 13:39 > To : simon.rit at creatis.insa-lyon.fr > Cc : emaddox at planet.nl, rtk-users at openrtk.org > Subject : RE: [Rtk-users] how can I get a good 3d image? > > > Oups. My bad, I didn?t know that. **** > > Thanks for your correction.**** > > ** ** > > *De :* simon.rit at gmail.com [mailto:simon.rit at gmail.com] *De la part de*Simon Rit > *Envoy? :* lundi 26 ao?t 2013 13:33 > *? :* MORY, CYRIL > *Cc :* emaddox at planet.nl; rtk-users at openrtk.org > *Objet :* Re: [Rtk-users] how can I get a good 3d image?**** > > ** ** > > Hi,**** > > Just a correction on Cyril's comment: there is a conversion to attenuation > with tif images, see > http://www.openrtk.org/Doxygen/classrtk_1_1TiffLookupTableImageFilter.html > **** > > It assumes that the maximum possible value is I0. You can check the result > with > rtkprojections -p. -r .*.tif -o proj.mha**** > > I think that the problem is that you don't define the position of your > rotation center with the --proj_iso_x and --proj_iso_y options in > rtksimulatedgeometry. If you don't set those, the rotation center on the > projection image is assumed to be the point of coordinate (0,0), i.e., the > first pixel of the image with tif images. The two above-mentioned options > allow to translate this point. > Simon**** > > ** ** > > On Mon, Aug 26, 2013 at 1:22 PM, MORY, CYRIL > wrote:**** > > Hi Erik, > > Judging from the projection image you sent, you seem to be missing a > crucial step. > > The area around your water cylinder is white and the cylinder itself is > black. This is the raw data you obtain from a scanner. It is (more or less) > the power received by each > pixel of the detector. Before you backproject this, you have to convert it > to attenuations. > > Check out the Wikipedia page > http://en.wikipedia.org/wiki/Tomographic_reconstruction. > Currently your images represent I, and you have to extract p. Only then > can you hope to get something coherent from an FDK reconstruction. > > Best regards, > Cyril > > -----Message d'origine----- > De : rtk-users-bounces at openrtk.org [mailto:rtk-users-bounces at openrtk.org] > De la part de emaddox at planet.nl > Envoy? : lundi 26 ao?t 2013 11:48 > ? : rtk-users at openrtk.org > Objet : [Rtk-users] how can I get a good 3d image?**** > > > Hi, > > I tried to reconstruct with RTK an example CT data set of a water phantom > but so far no success. > I carefully checked all hints on the website and looked to the examples > which I could run on my system. > > My data is acquired in a cone beam CT system. > > My projections are tif images, 103 images each rotated by 1.98 degree > steps. > The images are 640 by 512 pixels. > > Distances: source to detector is 255 mm, source to centre object is 200 mm > > commands I used: > > rtksimulatedgeometry.exe -n 103 -a 201.96 --sdd=255 --sid=200 -o > geometry.xml > > rtkfdk.exe -g geometry.xml -p water -r .*.tif -o water.mha --spacing=0.169 > > (I tried --dimension with single slice and all slices (640)) > > my projections: > > http://ubuntuone.com/4HZutj9lxgOZHydqBi0IM8 (30 Mb) > > can someone tell me if I can (and how to) get a good reconstruction with > RTK of this water phantom? > > Kind regards, > Erik Maddox. > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ________________________________ > The information contained in this message may be confidential and legally > protected under applicable law. The message is intended solely for the > addressee(s). If you are not the intended recipient, you are hereby > notified that any use, forwarding, dissemination, or reproduction of this > message is strictly prohibited and may be unlawful. If you are not the > intended recipient, please contact the sender by return e-mail and destroy > all copies of the original message.**** > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users**** > > ** ** > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: