From llgc at umich.edu Tue Jan 14 22:39:59 2014 From: llgc at umich.edu (Langechuan Liu) Date: Tue, 14 Jan 2014 22:39:59 -0500 Subject: [Rtk-users] use RTK to perform CBCT reconstruction of short scan Message-ID: Hello, I am new to RTK. Thanks to the creators for building such a great toolset. I found information about RTK because I was trying to perform a CBCT recon based on a short scan obtained from Varian OBI. In my specific case, I have 372 projection images (both in the original Varian .hnd format, and raw projection format converted with plastimatch) scanned over 220 degrees of the phantom. I have followed the instructions on the wiki page and successfully installed RTK. However I could not find much documentation regarding the parker short scan weighting tool. I did find some prompts after typing into command line: user at Cluster:~/RTK/RTK-bin/bin$ ./rtkparkershortscanweighting ./rtkparkershortscanweighting: '--geometry' ('-g') option required ./rtkparkershortscanweighting: '--path' ('-p') option required ./rtkparkershortscanweighting: '--regexp' ('-r') option required ./rtkparkershortscanweighting: '--output' ('-o') option required Judging from the name, I suppose this rtkparkershortscanweighting tool is to preprocess the projection data, but I am not sure. I am also puzzled at what I should specify for each of the options, especially the geometry option (how should I generate the geometry file, etc). I googled but to no avail. Could somebody direct me to a tutorial, or shed some light on the usage of the command line tool? Thanks very much! Best Regards, Patrick L. Liu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jean.hoskovec at gmail.com Tue Jan 14 23:03:09 2014 From: jean.hoskovec at gmail.com (Jan Hoskovec) Date: Wed, 15 Jan 2014 05:03:09 +0100 Subject: [Rtk-users] use RTK to perform CBCT reconstruction of short scan In-Reply-To: References: Message-ID: Hello, rtkparkershortscanweighting is indeed for preprocessing the projection data. I don't think there is a tutorial for it, if none of the scripts mentioned on wiki.openrtk.org matches your case (you'd better re-check that). To generate a geometry file, you will need to run rtksimulatedgeometry. Typing "rtksimulatedgeometry -h" should provide enough information, but I suggest you read http://www.creatis.insa-lyon.fr/~srit/geometry.pdf should you be confused about the geometric conventions. The -p and -r options specify the input file(s). The tool is designed to be able to treat multiple files at the same time, so you specify the directory (-p) and a file name pattern (-r) separately. If you have just one file in your current working directory that you want to treat, then you can type "-p . -r ". The -o option is quite straightforward, it's the name of the output image. Anyhow, all RTK command line binaries have a reasonably detailed help available if you launch them with the "-h" option. I hope these little hints will help you to find your way out. Don't worry, my first reconstruction with RTK was just about as chaotic. Regards, Jan 2014/1/15 Langechuan Liu : > Hello, > > I am new to RTK. Thanks to the creators for building such a great toolset. > > I found information about RTK because I was trying to perform a CBCT recon > based on a short scan obtained from Varian OBI. > > In my specific case, I have 372 projection images (both in the original > Varian .hnd format, and raw projection format converted with plastimatch) > scanned over 220 degrees of the phantom. > > I have followed the instructions on the wiki page and successfully installed > RTK. However I could not find much documentation regarding the parker short > scan weighting tool. I did find some prompts after typing into command line: > > user at Cluster:~/RTK/RTK-bin/bin$ ./rtkparkershortscanweighting > ./rtkparkershortscanweighting: '--geometry' ('-g') option required > ./rtkparkershortscanweighting: '--path' ('-p') option required > ./rtkparkershortscanweighting: '--regexp' ('-r') option required > ./rtkparkershortscanweighting: '--output' ('-o') option required > > Judging from the name, I suppose this rtkparkershortscanweighting tool is to > preprocess the projection data, but I am not sure. I am also puzzled at what > I should specify for each of the options, especially the geometry option > (how should I generate the geometry file, etc). I googled but to no avail. > > > Could somebody direct me to a tutorial, or shed some light on the usage of > the command line tool? > > Thanks very much! > > Best Regards, > Patrick L. Liu > > _______________________________________________ > 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 Wed Jan 15 01:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 15 Jan 2014 07:36:52 +0100 Subject: [Rtk-users] use RTK to perform CBCT reconstruction of short scan In-Reply-To: References:

Message-ID: Hi, Thanks for the kind words Patrick. To complement Jan's answer: - rtkparkershortscanweighting may be used to see the effect of the Parker weighting, - rtkfdk automatically triggers Parker weighting when it detects that the scan is short. There is a threshold in the Parker implementation for this, 20 degrees. See rtkParkerShortScanImageFilter.txx for more details. - you just have to add the option --arc to make the scan short, e.g., --arc=200. I have added a comment on the wiki about it: http://wiki.openrtk.org/index.php/RTK/Scripts/FDK Simon On Wed, Jan 15, 2014 at 5:03 AM, Jan Hoskovec wrote: > Hello, > > rtkparkershortscanweighting is indeed for preprocessing the projection > data. I don't think there is a tutorial for it, if none of the scripts > mentioned on wiki.openrtk.org matches your case (you'd better re-check > that). > > To generate a geometry file, you will need to run > rtksimulatedgeometry. Typing "rtksimulatedgeometry -h" should provide > enough information, but I suggest you read > http://www.creatis.insa-lyon.fr/~srit/geometry.pdf should you be > confused about the geometric conventions. > > The -p and -r options specify the input file(s). The tool is designed > to be able to treat multiple files at the same time, so you specify > the directory (-p) and a file name pattern (-r) separately. If you > have just one file in your current working directory that you want to > treat, then you can type "-p . -r ". The -o option is > quite straightforward, it's the name of the output image. > > Anyhow, all RTK command line binaries have a reasonably detailed help > available if you launch them with the "-h" option. > > I hope these little hints will help you to find your way out. Don't > worry, my first reconstruction with RTK was just about as chaotic. > > Regards, > > Jan > > 2014/1/15 Langechuan Liu : >> Hello, >> >> I am new to RTK. Thanks to the creators for building such a great toolset. >> >> I found information about RTK because I was trying to perform a CBCT recon >> based on a short scan obtained from Varian OBI. >> >> In my specific case, I have 372 projection images (both in the original >> Varian .hnd format, and raw projection format converted with plastimatch) >> scanned over 220 degrees of the phantom. >> >> I have followed the instructions on the wiki page and successfully installed >> RTK. However I could not find much documentation regarding the parker short >> scan weighting tool. I did find some prompts after typing into command line: >> >> user at Cluster:~/RTK/RTK-bin/bin$ ./rtkparkershortscanweighting >> ./rtkparkershortscanweighting: '--geometry' ('-g') option required >> ./rtkparkershortscanweighting: '--path' ('-p') option required >> ./rtkparkershortscanweighting: '--regexp' ('-r') option required >> ./rtkparkershortscanweighting: '--output' ('-o') option required >> >> Judging from the name, I suppose this rtkparkershortscanweighting tool is to >> preprocess the projection data, but I am not sure. I am also puzzled at what >> I should specify for each of the options, especially the geometry option >> (how should I generate the geometry file, etc). I googled but to no avail. >> >> >> Could somebody direct me to a tutorial, or shed some light on the usage of >> the command line tool? >> >> Thanks very much! >> >> Best Regards, >> Patrick L. Liu >> >> _______________________________________________ >> 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 llgc at umich.edu Wed Jan 15 22:41:10 2014 From: llgc at umich.edu (Langechuan Liu) Date: Wed, 15 Jan 2014 22:41:10 -0500 Subject: [Rtk-users] use RTK to perform CBCT reconstruction of short scan In-Reply-To: References:

Message-ID: Thanks, Jan and Simon! I really appreciate your fast reply and kind help. With your guidance I finally get the reconstruction tool rtkfdk to work after experimenting it for several hours. Now I have some new questions regarding this tool. 1. one of the options for rtkfdk is the --spacing, with default value set to 1. Correct me if I am wrong, I suppose this specifies the spatial distance between elements of the reconstructed 3d matrix (in unit of mm), but does this also corresponds to the thickness of projection images used to reconstruct that slice? In other words, if there are two reconstructions, with options: case 1: (--spacing 0.25,1.25,0.25 --dimension 1024,1,1024) case 2: (--spacing 0.25,0.25,0.25 --dimension 1024,5,1024) Is it true that the single slice in case 1 is equivalent of the summation of the 5 slices of case 2, or equivalent to the central slice (3rd one) in case 2? 2. another option is the origin. I am not sure I totally understand why this option is specified as --origin -127.875,30,-127.875 in the 3rd step of the following varian recon example in wiki. http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction My guess is that 30 is needed because only one slice 30 mm off center is to be reconstructed, and -127.875 is to ensure x-y direction is "centered" (which equals to the default value)? It is a bit odd to me that the default origin value is not 0,0,0. Could anybody comment on these two points? Or direct me to the place where I could learn about these details? Thanks very much! Patrick L. Liu On Wed, Jan 15, 2014 at 1:36 AM, Simon Rit wrote: > Hi, > Thanks for the kind words Patrick. To complement Jan's answer: > - rtkparkershortscanweighting may be used to see the effect of the > Parker weighting, > - rtkfdk automatically triggers Parker weighting when it detects that > the scan is short. There is a threshold in the Parker implementation > for this, 20 degrees. See rtkParkerShortScanImageFilter.txx for more > details. > - you just have to add the option --arc to make the scan short, e.g., > --arc=200. I have added a comment on the wiki about it: > http://wiki.openrtk.org/index.php/RTK/Scripts/FDK > Simon > > On Wed, Jan 15, 2014 at 5:03 AM, Jan Hoskovec > wrote: > > Hello, > > > > rtkparkershortscanweighting is indeed for preprocessing the projection > > data. I don't think there is a tutorial for it, if none of the scripts > > mentioned on wiki.openrtk.org matches your case (you'd better re-check > > that). > > > > To generate a geometry file, you will need to run > > rtksimulatedgeometry. Typing "rtksimulatedgeometry -h" should provide > > enough information, but I suggest you read > > http://www.creatis.insa-lyon.fr/~srit/geometry.pdf should you be > > confused about the geometric conventions. > > > > The -p and -r options specify the input file(s). The tool is designed > > to be able to treat multiple files at the same time, so you specify > > the directory (-p) and a file name pattern (-r) separately. If you > > have just one file in your current working directory that you want to > > treat, then you can type "-p . -r ". The -o option is > > quite straightforward, it's the name of the output image. > > > > Anyhow, all RTK command line binaries have a reasonably detailed help > > available if you launch them with the "-h" option. > > > > I hope these little hints will help you to find your way out. Don't > > worry, my first reconstruction with RTK was just about as chaotic. > > > > Regards, > > > > Jan > > > > 2014/1/15 Langechuan Liu : > >> Hello, > >> > >> I am new to RTK. Thanks to the creators for building such a great > toolset. > >> > >> I found information about RTK because I was trying to perform a CBCT > recon > >> based on a short scan obtained from Varian OBI. > >> > >> In my specific case, I have 372 projection images (both in the original > >> Varian .hnd format, and raw projection format converted with > plastimatch) > >> scanned over 220 degrees of the phantom. > >> > >> I have followed the instructions on the wiki page and successfully > installed > >> RTK. However I could not find much documentation regarding the parker > short > >> scan weighting tool. I did find some prompts after typing into command > line: > >> > >> user at Cluster:~/RTK/RTK-bin/bin$ ./rtkparkershortscanweighting > >> ./rtkparkershortscanweighting: '--geometry' ('-g') option required > >> ./rtkparkershortscanweighting: '--path' ('-p') option required > >> ./rtkparkershortscanweighting: '--regexp' ('-r') option required > >> ./rtkparkershortscanweighting: '--output' ('-o') option required > >> > >> Judging from the name, I suppose this rtkparkershortscanweighting tool > is to > >> preprocess the projection data, but I am not sure. I am also puzzled at > what > >> I should specify for each of the options, especially the geometry option > >> (how should I generate the geometry file, etc). I googled but to no > avail. > >> > >> > >> Could somebody direct me to a tutorial, or shed some light on the usage > of > >> the command line tool? > >> > >> Thanks very much! > >> > >> Best Regards, > >> Patrick L. Liu > >> > >> _______________________________________________ > >> 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 -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jan 16 03:19:38 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 16 Jan 2014 09:19:38 +0100 Subject: [Rtk-users] use RTK to perform CBCT reconstruction of short scan In-Reply-To: References:

Message-ID: On Thu, Jan 16, 2014 at 4:21 AM, Patrick Langechuan LIU wrote: > Thanks, Jan and Simon! > > I really appreciate your fast reply and kind help. With your guidance I > finally get the reconstruction tool rtkfdk to work after experimenting it > for several hours. Now I have some new questions regarding this tool. > > 1. one of the options for rtkfdk is the --spacing, with default value set to > 1. Correct me if I am wrong, I suppose this specifies the spatial distance > between elements of the reconstructed 3d matrix (in unit of mm), but does > this also corresponds to the thickness of projection images used to > reconstruct that slice? In other words, if there are two reconstructions, > with options: > case 1: (--spacing 0.25,1.25,0.25 --dimension 1024,1,1024) > case 2: (--spacing 0.25,0.25,0.25 --dimension 1024,5,1024) > > Is it true that the single slice in case 1 is equivalent of the summation of > the 5 slices of case 2, or equivalent to the central slice (3rd one) in case > 2? No, it's not true. It defines the position of the voxels which does not mean that it will sum the 5 slices. In your example, the central slice of case 2 equal the single slice of case 1, not the sum. > > > 2. another option is the origin. I am not sure I totally understand why this > option is specified as > --origin -127.875,30,-127.875 > in the 3rd step of the following varian recon example in wiki. > http://wiki.openrtk.org/index.php/RTK/Examples/VarianReconstruction > > My guess is that 30 is needed because only one slice 30 mm off center is to > be reconstructed, and -127.875 is to ensure x-y direction is "centered" > (which equals to the default value)? It is a bit odd to me that the default > origin value is not 0,0,0. > > Could anybody comment on these two points? Or direct me to the place where I > could learn about these details? You should study a bit ITK for this, it's not a RTK-specific question. In a few words, the spatial positions of voxels in ITK is defined by the origin, the spacing and the direction. The origin is the coordinate of the first voxel in memory, i.e., the inferior corner of your image in every direction (inferior assumes positive spacing and identity directions). So if you want to center a 4X4 image with 2x2 pixel spacing aroung the position 0,0 as, I guess, you want to, then the coordinate of the corner of your image should be -3,-3. You can look at slide 19 of this presentation for a scheme: www.cs.cmu.edu/~galeotti/methods_course/Lecture16-ITKImages.pptx I hope this helps, Simon > > Thanks very much! > > Patrick L. Liu > > > > > On Wed, Jan 15, 2014 at 1:36 AM, Simon Rit > wrote: >> >> Hi, >> Thanks for the kind words Patrick. To complement Jan's answer: >> - rtkparkershortscanweighting may be used to see the effect of the >> Parker weighting, >> - rtkfdk automatically triggers Parker weighting when it detects that >> the scan is short. There is a threshold in the Parker implementation >> for this, 20 degrees. See rtkParkerShortScanImageFilter.txx for more >> details. >> - you just have to add the option --arc to make the scan short, e.g., >> --arc=200. I have added a comment on the wiki about it: >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK >> Simon >> >> On Wed, Jan 15, 2014 at 5:03 AM, Jan Hoskovec >> wrote: >> > Hello, >> > >> > rtkparkershortscanweighting is indeed for preprocessing the projection >> > data. I don't think there is a tutorial for it, if none of the scripts >> > mentioned on wiki.openrtk.org matches your case (you'd better re-check >> > that). >> > >> > To generate a geometry file, you will need to run >> > rtksimulatedgeometry. Typing "rtksimulatedgeometry -h" should provide >> > enough information, but I suggest you read >> > http://www.creatis.insa-lyon.fr/~srit/geometry.pdf should you be >> > confused about the geometric conventions. >> > >> > The -p and -r options specify the input file(s). The tool is designed >> > to be able to treat multiple files at the same time, so you specify >> > the directory (-p) and a file name pattern (-r) separately. If you >> > have just one file in your current working directory that you want to >> > treat, then you can type "-p . -r ". The -o option is >> > quite straightforward, it's the name of the output image. >> > >> > Anyhow, all RTK command line binaries have a reasonably detailed help >> > available if you launch them with the "-h" option. >> > >> > I hope these little hints will help you to find your way out. Don't >> > worry, my first reconstruction with RTK was just about as chaotic. >> > >> > Regards, >> > >> > Jan >> > >> > 2014/1/15 Langechuan Liu : >> >> Hello, >> >> >> >> I am new to RTK. Thanks to the creators for building such a great >> >> toolset. >> >> >> >> I found information about RTK because I was trying to perform a CBCT >> >> recon >> >> based on a short scan obtained from Varian OBI. >> >> >> >> In my specific case, I have 372 projection images (both in the original >> >> Varian .hnd format, and raw projection format converted with >> >> plastimatch) >> >> scanned over 220 degrees of the phantom. >> >> >> >> I have followed the instructions on the wiki page and successfully >> >> installed >> >> RTK. However I could not find much documentation regarding the parker >> >> short >> >> scan weighting tool. I did find some prompts after typing into command >> >> line: >> >> >> >> user at Cluster:~/RTK/RTK-bin/bin$ ./rtkparkershortscanweighting >> >> ./rtkparkershortscanweighting: '--geometry' ('-g') option required >> >> ./rtkparkershortscanweighting: '--path' ('-p') option required >> >> ./rtkparkershortscanweighting: '--regexp' ('-r') option required >> >> ./rtkparkershortscanweighting: '--output' ('-o') option required >> >> >> >> Judging from the name, I suppose this rtkparkershortscanweighting tool >> >> is to >> >> preprocess the projection data, but I am not sure. I am also puzzled at >> >> what >> >> I should specify for each of the options, especially the geometry >> >> option >> >> (how should I generate the geometry file, etc). I googled but to no >> >> avail. >> >> >> >> >> >> Could somebody direct me to a tutorial, or shed some light on the usage >> >> of >> >> the command line tool? >> >> >> >> Thanks very much! >> >> >> >> Best Regards, >> >> Patrick L. Liu >> >> >> >> _______________________________________________ >> >> 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 liupeng_cs at 163.com Mon Jan 20 04:06:32 2014 From: liupeng_cs at 163.com (=?GBK?B?wfXF9A==?=) Date: Mon, 20 Jan 2014 17:06:32 +0800 (CST) Subject: [Rtk-users] Fix the issue when use RTK on Nvidia Kepler Architecture based GPU. Message-ID: <7a65d40d.154f5.143aee6b837.Coremail.liupeng_cs@163.com> Hello, I find an issue when I try to use RTK on a Nvidia Kepler based GPU. The CUDA initializing always fails. And I can see an exception about _cudaMutexOperation when any CUDA function is called in debug mode. Exception at 0x7fefd5f940d, code: 0xe06d7363: C++ exception, flags=0x1 (execution cannot be continued) (first chance) in cudart64_50_35!_cudaMutexOperation Following the guide in http://docs.nvidia.com/cuda/kepler-compatibility-guide/index.html This issue can be fixed by applying the patch on RTK code: =========================================================================== diff --git a/cmake/FindCUDA_wrap.cmake b/cmake/FindCUDA_wrap.cmake index e13a7c3..b40c6da 100644 --- a/cmake/FindCUDA_wrap.cmake +++ b/cmake/FindCUDA_wrap.cmake @@ -59,9 +59,19 @@ set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} ) if(CUDA_VERSION_MAJOR GREATER "2") - set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} - -gencode arch=compute_20,code=sm_20 - ) + IF(${CUDA_VERSION} LESS 5.0) + set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} + -gencode arch=compute_20,code=sm_20 + -gencode arch=compute_20,code=compute_20 + ) + ELSE() + set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} + -gencode arch=compute_20,code=sm_20 + -gencode arch=compute_30,code=sm_30 + -gencode arch=compute_35,code=sm_35 + -gencode arch=compute_35,code=compute_35 + ) + ENDIF() endif() if(CUDA_FOUND) ============================================================================ Regards, Peng Liu -------------- next part -------------- An HTML attachment was scrubbed... URL: From llgc at umich.edu Tue Jan 14 22:39:59 2014 From: llgc at umich.edu (Langechuan Liu) Date: Tue, 14 Jan 2014 22:39:59 -0500 Subject: [Rtk-users] use RTK to perform CBCT reconstruction of short scan Message-ID: Hello, I am new to RTK. Thanks to the creators for building such a great toolset. I found information about RTK because I was trying to perform a CBCT recon based on a short scan obtained from Varian OBI. In my specific case, I have 372 projection images (both in the original Varian .hnd format, and raw projection format converted with plastimatch) scanned over 220 degrees of the phantom. I have followed the instructions on the wiki page and successfully installed RTK. However I could not find much documentation regarding the parker short scan weighting tool. I did find some prompts after typing into command line: user at Cluster:~/RTK/RTK-bin/bin$ ./rtkparkershortscanweighting ./rtkparkershortscanweighting: '--geometry' ('-g') option required ./rtkparkershortscanweighting: '--path' ('-p') option required ./rtkparkershortscanweighting: '--regexp' ('-r') option required ./rtkparkershortscanweighting: '--output' ('-o') option required Judging from the name, I suppose this rtkparkershortscanweighting tool is to preprocess the projection data, but I am not sure. I am also puzzled at what I should specify for each of the options, especially the geometry option (how should I generate the geometry file, etc). I googled but to no avail. Could somebody direct me to a tutorial, or shed some light on the usage of the command line tool? Thanks very much! Best Regards, Patrick L. Liu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jean.hoskovec at gmail.com Tue Jan 14 23:03:09 2014 From: jean.hoskovec at gmail.com (Jan Hoskovec) Date: Wed, 15 Jan 2014 05:03:09 +0100 Subject: [Rtk-users] use RTK to perform CBCT reconstruction of short scan In-Reply-To: References: Message-ID: Hello, rtkparkershortscanweighting is indeed for preprocessing the projection data. I don't think there is a tutorial for it, if none of the scripts mentioned on wiki.openrtk.org matches your case (you'd better re-check that). To generate a geometry file, you will need to run rtksimulatedgeometry. Typing "rtksimulatedgeometry -h" should provide enough information, but I suggest you read http://www.creatis.insa-lyon.fr/~srit/geometry.pdf should you be confused about the geometric conventions. The -p and -r options specify the input file(s). The tool is designed to be able to treat multiple files at the same time, so you specify the directory (-p) and a file name pattern (-r) separately. If you have just one file in your current working directory that you want to treat, then you can type "-p . -r ". The -o option is quite straightforward, it's the name of the output image. Anyhow, all RTK command line binaries have a reasonably detailed help available if you launch them with the "-h" option. I hope these little hints will help you to find your way out. Don't worry, my first reconstruction with RTK was just about as chaotic. Regards, Jan 2014/1/15 Langechuan Liu : > Hello, > > I am new to RTK. Thanks to the creators for building such a great toolset. > > I found information about RTK because I was trying to perform a CBCT recon > based on a short scan obtained from Varian OBI. > > In my specific case, I have 372 projection images (both in the original > Varian .hnd format, and raw projection format converted with plastimatch) > scanned over 220 degrees of the phantom. > > I have followed the instructions on the wiki page and successfully installed > RTK. However I could not find much documentation regarding the parker short > scan weighting tool. I did find some prompts after typing into command line: > > user at Cluster:~/RTK/RTK-bin/bin$ ./rtkparkershortscanweighting > ./rtkparkershortscanweighting: '--geometry' ('-g') option required > ./rtkparkershortscanweighting: '--path' ('-p') option required > ./rtkparkershortscanweighting: '--regexp' ('-r') option required > ./rtkparkershortscanweighting: '--output' ('-o') option required > > Judging from the name, I suppose this rtkparkershortscanweighting tool is to > preprocess the projection data, but I am not sure. I am also puzzled at what > I should specify for each of the options, especially the geometry option > (how should I generate the geometry file, etc). I googled but to no avail. > > > Could somebody direct me to a tutorial, or shed some light on the usage of > the command line tool? > > Thanks very much! > > Best Regards, > Patrick L. Liu > > _______________________________________________ > 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 Wed Jan 15 01:36:52 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 15 Jan 2014 07:36:52 +0100 Subject: [Rtk-users] use RTK to perform CBCT reconstruction of short scan In-Reply-To: References: