From simon.rit at creatis.insa-lyon.fr Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > 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 Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > 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 Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > 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 Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > 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 Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > 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 Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > 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 Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > 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 Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > 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 Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > 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 Sat Feb 2 13:47:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sat, 2 Feb 2013 19:47:37 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Dear Wen, I don't mind, that's why the project is open source! I think raw images are already available via itk, you just have to create a mhd header that points to that raw file. Look here for more information: http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some information in a header or a joint file, you may want to do specific I/O objects for Siemens. This is explained on the ITK documentation. In my experience, it's hard to obtain information from constructor and you have to guess or measure it yourself. In some cases, you even want to do better than the constructor. However, the more information you can get from them, the better. For example, I know I do something close to the constructor for Elekta but I don't know how good is my Varian stuff. I get the geometry from their files, it's usually simple to understand. We may be able to help you if you can provide a sample acquisition. Discussions for RTK are done via the mailing list (cc), you can suscribe on the website. There is also a wiki (click on help). There are examples you can use there and some data are available on the RTK midas community. I hope this helps. Let me know if I can do more, Simon On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: > Hi Simon, > > I hope you don't mind a random email regarding RTK. I'm a CS PhD student at > Johns Hopkins working on integrating CBCT with medical robotics. We have a > Siemen's C-arm system that provides raw (16 bit unsigned short) images that > I wish to process and reconstruction using RTK. I've noticed your authorship > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process platform > specific outputs into projections/attuentation images that RTK can > reconstruct. What would you recommend as my next steps? Port in raw images > to RTK? Consult with Siemen's regarding their calibration data to map raw to > attenuation? Is this typically done with lookup tables, i.e. based on > geometric and calibration? > > Also if there are literature, discussion groups for RTK and these topics, > please point me in the right direction! > > Thanks very much for your time and help. > > Regards, > Wen > > https://www.lcsr.jhu.edu/User:Wliu25 From simon.rit at creatis.insa-lyon.fr Mon Feb 11 01:48:07 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Mon, 11 Feb 2013 07:48:07 +0100 Subject: [Rtk-users] Question regarding RTK In-Reply-To: References: Message-ID: Hi Wen, The offsets values depend on where the origin of the coordinate system of your projections. With all angles at 0, the offsets give the coordinates in the projection of the ray passing through the source and the isocenter. There are some explanations on the wiki for the geometry, it might help. You might want to try using rtk::Reg23ProjectionGeometry. It is a child of the other geometry with a different parameterization which uses the row and column vectors of your projection images in the coordinate system of the tomography to be reconstructed. It is probably quite straightforward to extract this from your matrices. Let us know if you can't figure it out, I will have a look then at your data. Good luck! Simon On Wed, Feb 6, 2013 at 9:41 PM, Wen P. Liu wrote: > Hi Simon, > > Thanks for the quick reply and the positivity! I was able to reconstruct > (using SART) with raw and some simple rawToAttenuation projections (see .png > in attachment). Through trial and error I found that setting the offset to > image center was key. The dislocations of the sphere in reconstruction is > probably due to my assumption of circular trajectories. I have the 3Dto2D > projection matrices from Siemens for each angle that would project isocenter > coordinates to detector but found that RTK is expecting the transformation > at the source and detector (3DCircularProjectionGeometry->AddProjection()). > If I wanted to inject these projection matrices directly into reconstruction > what steps would you recommend? Thanks very much for your time. Just FYI I'm > going to email the mailing list (minus the data) with the same question. > > Regards, > Wen > > > On Sat, Feb 2, 2013 at 10:47 AM, Simon Rit > wrote: >> >> Dear Wen, >> I don't mind, that's why the project is open source! I think raw >> images are already available via itk, you just have to create a mhd >> header that points to that raw file. Look here for more information: >> http://www.itk.org/Wiki/ITK/File_Formats. However, if there is some >> information in a header or a joint file, you may want to do specific >> I/O objects for Siemens. This is explained on the ITK documentation. >> In my experience, it's hard to obtain information from constructor and >> you have to guess or measure it yourself. In some cases, you even want >> to do better than the constructor. However, the more information you >> can get from them, the better. For example, I know I do something >> close to the constructor for Elekta but I don't know how good is my >> Varian stuff. I get the geometry from their files, it's usually simple >> to understand. We may be able to help you if you can provide a sample >> acquisition. >> Discussions for RTK are done via the mailing list (cc), you can >> suscribe on the website. There is also a wiki (click on help). There >> are examples you can use there and some data are available on the RTK >> midas community. >> I hope this helps. Let me know if I can do more, >> Simon >> >> On Sat, Feb 2, 2013 at 5:45 AM, Wen Liu wrote: >> > Hi Simon, >> > >> > I hope you don't mind a random email regarding RTK. I'm a CS PhD student >> > at >> > Johns Hopkins working on integrating CBCT with medical robotics. We have >> > a >> > Siemen's C-arm system that provides raw (16 bit unsigned short) images >> > that >> > I wish to process and reconstruction using RTK. I've noticed your >> > authorship >> > on several classes (rtkImageXxxx, rtkVarianxxx, etc) which process >> > platform >> > specific outputs into projections/attuentation images that RTK can >> > reconstruct. What would you recommend as my next steps? Port in raw >> > images >> > to RTK? Consult with Siemen's regarding their calibration data to map >> > raw to >> > attenuation? Is this typically done with lookup tables, i.e. based on >> > geometric and calibration? >> > >> > Also if there are literature, discussion groups for RTK and these >> > topics, >> > please point me in the right direction! >> > >> > Thanks very much for your time and help. >> > >> > Regards, >> > Wen >> > >> > https://www.lcsr.jhu.edu/User:Wliu25 > > From Cyril.Mory at philips.com Wed Feb 13 04:21:37 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 09:21:37 +0000 Subject: [Rtk-users] ITK cmake settings Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi, I'm reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK were recommended for the use of RTK. The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't give any more advice. So here are my questions (some of which probably have nothing to do with RTK, sorry) : - What about the FFTW-related options ? RTK uses FFTW to ramp-filter the projections, right ? Should I activate the single precision or the double precision FFTW ? (I tried activating both, it lead to some kind of conflict and the linker couldn't find the libraries) - In order to be able to track an error in my RTK code and see where it crashes in ITK, do I need to compile ITK in Debug mode ? - Do you have recommendations about the BUILD_SHARED_LIBRARIES option (other than the simple difference between shared and static libraries) ? - Anything else ? 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Wed Feb 13 04:47:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 10:47:49 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I?m reinstalling ITK and RTK, and I was wondering which CMAKE options in ITK > were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn?t give > any more advice. > > > > So here are my questions (some of which probably have nothing to do with > RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single precision > or the double precision FFTW ? (I tried activating both, it lead to some > kind of conflict and the linker couldn?t find the libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 Cyril.Mory at philips.com Wed Feb 13 05:09:46 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 10:09:46 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F450E0@011-DB3MPN1-043.MGDPHG.emi.philips.com> THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 Cyril.Mory at philips.com Wed Feb 13 06:04:23 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 11:04:23 +0000 Subject: [Rtk-users] ITK cmake settings References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. So I tried it all again. And the popped : I have used the following non-default CMAKE options : CMAKE_BUILDE_TYPE : Debug ITK_USE_64BITS_IDS : ON ITK_USE_FFTWD : ON ITK_USE_FFTWF : ON ITK_USE_REVIEW : ON This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. Here is the error : [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. Cyril -----Message d'origine----- De : MORY, CYRIL Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' Cc : rtk-users at openrtk.org Objet : RE: [Rtk-users] ITK cmake settings THanks for your answers Simon, Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. I used the FFTW shipped with ITK4, not a system fftw. During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. Cyril -----Message d'origine----- De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings Hi Cyril, Very good questions. ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. Don't hesitate to report any other option that we would have overlooked. Simon On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > Hi, > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > in ITK were recommended for the use of RTK. > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > give any more advice. > > > > So here are my questions (some of which probably have nothing to do > with RTK, sorry) : > > > > - What about the FFTW-related options ? RTK uses FFTW to > ramp-filter the projections, right ? Should I activate the single > precision or the double precision FFTW ? (I tried activating both, it > lead to some kind of conflict and the linker couldn't find the > libraries) > > - In order to be able to track an error in my RTK code and see > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > option (other than the simple difference between shared and static > libraries) ? > > - Anything else ? > > > > 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 > ________________________________ 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 marc.vila-oliva at creatis.insa-lyon.fr Wed Feb 13 06:57:24 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Wed, 13 Feb 2013 12:57:24 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> Message-ID: <1360756645.2294.40.camel@mvila-laptop> Hei Cyril, There are known issues with ITK compiling with gcc-4.7. Can you try your same configuration using an older version of gcc and g++? I will try to compile ITK with your same set up and I'll let you know. Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 > ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options > > in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't > > give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, it > > lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 Wed Feb 13 07:51:35 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Wed, 13 Feb 2013 13:51:35 +0100 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: Hi Cyril, Same here, I compiled with the same parameters and it went fine. I would advise you to move to the ITK mailing list since the problem is not RTK related... and there are more people there able to help you. Good luck, Simon On Wed, Feb 13, 2013 at 1:23 PM, Marc Vila Oliva wrote: > Hello again! > > I just compiled ITK 4.3.0 in Debug mode with the following set up (check > CMakeCache.txt) > > My compilers gcc-4.5.2 & c++-4.5.2. > > I hope it helps! > > Cheers, > Marc > > On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: >> Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. >> For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. >> >> So I tried it all again. And the popped : >> >> I have used the following non-default CMAKE options : >> CMAKE_BUILDE_TYPE : Debug >> ITK_USE_64BITS_IDS : ON >> ITK_USE_FFTWD : ON >> ITK_USE_FFTWF : ON >> ITK_USE_REVIEW : ON >> >> This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. >> >> Here is the error : >> >> [ 69%] Building CXX object Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorImageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3_threads >> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld: cannot find -lfftw3f_threads >> >> And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : >> >> drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ >> drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ >> -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a >> -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a >> -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* >> -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a >> -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* >> -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* >> -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a >> -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* >> drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ >> >> >> I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. >> Cyril >> >> -----Message d'origine----- >> De : MORY, CYRIL >> Envoy? : mercredi 13 f?vrier 2013 11:10 >> ? : 'Simon Rit' >> Cc : rtk-users at openrtk.org >> Objet : RE: [Rtk-users] ITK cmake settings >> >> THanks for your answers Simon, >> >> Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. >> I used the FFTW shipped with ITK4, not a system fftw. >> During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. >> >> Cyril >> >> >> -----Message d'origine----- >> De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings >> >> Hi Cyril, >> Very good questions. >> >> ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. >> >> It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? >> >> In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. >> >> There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. >> You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. >> >> I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. >> Don't hesitate to report any other option that we would have overlooked. >> Simon >> >> On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: >> > Hi, >> > >> > >> > >> > I'm reinstalling ITK and RTK, and I was wondering which CMAKE options >> > in ITK were recommended for the use of RTK. >> > >> > The wiki says to switch ITK_USE_REVIEW on, which I did, but it doesn't >> > give any more advice. >> > >> > >> > >> > So here are my questions (some of which probably have nothing to do >> > with RTK, sorry) : >> > >> > >> > >> > - What about the FFTW-related options ? RTK uses FFTW to >> > ramp-filter the projections, right ? Should I activate the single >> > precision or the double precision FFTW ? (I tried activating both, it >> > lead to some kind of conflict and the linker couldn't find the >> > libraries) >> > >> > - In order to be able to track an error in my RTK code and see >> > where it crashes in ITK, do I need to compile ITK in Debug mode ? >> > >> > - Do you have recommendations about the BUILD_SHARED_LIBRARIES >> > option (other than the simple difference between shared and static >> > libraries) ? >> > >> > - Anything else ? >> > >> > >> > >> > 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 >> > >> >> ________________________________ >> 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 Cyril.Mory at philips.com Wed Feb 13 07:57:55 2013 From: Cyril.Mory at philips.com (MORY, CYRIL) Date: Wed, 13 Feb 2013 12:57:55 +0000 Subject: [Rtk-users] ITK cmake settings In-Reply-To: <1360758202.2294.43.camel@mvila-laptop> References: <3B67D2F1029933428E0E93E2C2F1801334F4509A@011-DB3MPN1-043.MGDPHG.emi.philips.com> <3B67D2F1029933428E0E93E2C2F1801334F45132@011-DB3MPN1-043.MGDPHG.emi.philips.com> <1360758202.2294.43.camel@mvila-laptop> Message-ID: <3B67D2F1029933428E0E93E2C2F1801334F451CD@011-DB3MPN1-043.MGDPHG.emi.philips.com> Hi Marc, I recompiled ITK with gcc-4.3 & g++-4.3, but the same problem occurred. I found a fix, though : The libraries libfftw3f_threads.so.3 and libfftw3_threads.so.3 were in my /usr/lib64 directory (I think they got there when I compiled with BUILD_SHARED_LIBS on), but there was no symbolic link from libfftw3f_threads.so and libfftw3_threads.so So I manually created them using : sudo ln -s libfftw3f_threads.so.3 libfftw3f_threads.so sudo ln -s libfftw3_threads.so.3 libfftw3_threads.so And everything compiled magically (even the tests). So I'm inclined to think that it's only a problem with some CMAKE function not creating the symbolic links required. I'll report this to Kitware. Thanks for your help anyway -----Message d'origine----- De?: Marc Vila Oliva [mailto:marc.vila-oliva at creatis.insa-lyon.fr] Envoy??: mercredi 13 f?vrier 2013 13:23 ??: MORY, CYRIL Cc?: Simon Rit; rtk-users at openrtk.org Objet?: Re: [Rtk-users] ITK cmake settings Hello again! I just compiled ITK 4.3.0 in Debug mode with the following set up (check CMakeCache.txt) My compilers gcc-4.5.2 & c++-4.5.2. I hope it helps! Cheers, Marc On Wed, 2013-02-13 at 11:04 +0000, MORY, CYRIL wrote: > Oups. I realized that the "successful" ITK compilation had the fftw flags set to off. > For some reason, when you change the compiler, and configure, CMAKE resets all the flags to their default values and you have to set them again. I hadn't noticed and had compiled without fftw, which is why it compiled fine. > > So I tried it all again. And the popped : > > I have used the following non-default CMAKE options : > CMAKE_BUILDE_TYPE : Debug > ITK_USE_64BITS_IDS : ON > ITK_USE_FFTWD : ON > ITK_USE_FFTWF : ON > ITK_USE_REVIEW : ON > > This time I have left BUILD_SHARED_LIBRARIES set to OFF in order to stick as much as possible to your configuration. > > Here is the error : > > [ 69%] Building CXX object > Modules/Filtering/DiffusionTensorImage/CMakeFiles/ITKDiffusionTensorIm > ageHeaderTest1.dir/test/ITKDiffusionTensorImageHeaderTest1.cxx.o > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3_threads > /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin > /ld: cannot find -lfftw3f_threads > > And the build directory contains three fftw-related directories : "fftw", "fftwf" and "fftwd". The libraries seem to be all in "fftw". Here is the content of "fftw/lib64" : > > drwxr-xr-x 3 cyril users 4096 Feb 13 11:43 ./ > drwxr-xr-x 6 cyril users 4096 Feb 13 11:42 ../ > -rw-r--r-- 1 cyril users 2792444 Feb 13 11:42 libfftw3.a > -rw-r--r-- 1 cyril users 2768478 Feb 13 11:43 libfftw3f.a > -rwxr-xr-x 1 cyril users 916 Feb 13 11:43 libfftw3f.la* > -rw-r--r-- 1 cyril users 48414 Feb 13 11:43 libfftw3f_threads.a > -rwxr-xr-x 1 cyril users 1003 Feb 13 11:43 libfftw3f_threads.la* > -rwxr-xr-x 1 cyril users 913 Feb 13 11:42 libfftw3.la* > -rw-r--r-- 1 cyril users 48272 Feb 13 11:42 libfftw3_threads.a > -rwxr-xr-x 1 cyril users 999 Feb 13 11:42 libfftw3_threads.la* > drwxr-xr-x 2 cyril users 4096 Feb 13 11:43 pkgconfig/ > > > I'm running OpenSuse 12.2 64 bits, using gcc 4.7 and g++ 4.7, in case it matters. > Cyril > > -----Message d'origine----- > De : MORY, CYRIL > Envoy? : mercredi 13 f?vrier 2013 11:10 ? : 'Simon Rit' > Cc : rtk-users at openrtk.org > Objet : RE: [Rtk-users] ITK cmake settings > > THanks for your answers Simon, > > Regarding the "conflict" I experienced : I have changed to only single precision FFTW, and it solved my problem, so I can't tell you more than what I remember. > I used the FFTW shipped with ITK4, not a system fftw. > During the compilation of ITK, the linking of some executable crashed, saying it couldn't locate "libfftw3f_threads" and "libfftw3_threads". I checked the itk build directory and these libraries were built correctly, but for some reason the linker couldn't find them. I thought that the CMAKE option to locate one could somehow be overwritten by the other, activated only the single precision one, emptied the build directory to clean the cache, and restarted the build. It built correctly. > > Cyril > > > -----Message d'origine----- > De : simon.rit at gmail.com [mailto:simon.rit at gmail.com] De la part de > Simon Rit Envoy? : mercredi 13 f?vrier 2013 10:48 ? : MORY, CYRIL Cc : > rtk-users at openrtk.org Objet : Re: [Rtk-users] ITK cmake settings > > Hi Cyril, > Very good questions. > > ITK_USE_REVIEW is ITK 3.20 related, I don't think it is required in ITK 4. > > It is very much advised to use FFTW because it is faster and more flexible in terms of projection dimensions. Both single and double precision can be turned on. It works for me, can you send us a report on the conflict you get? Do you use the system fftw or you let ITK4 download it? > > In order to track bugs in your code, yes, you need to compile ITK with debug or RelWithDebInfo because the crash might be in the itk part and even if not, the compilation might be difficult (if possible) with itk in release and rtk in debug. > > There is no recommendation with shared libraries except that we have encountered difficulties in the past with shared libraries and cuda. > You'll probably have to add a -fPIC options to make it work. I am used to use static libraries by default but I don't have a real good argument for this. > > I would also recommend turning off BUILD_EXAMPLES and BUILD_TESTING for rapidity and ITK_BUILD_ALL_MODULES in itk4 to be sure that you have everything required. > Don't hesitate to report any other option that we would have overlooked. > Simon > > On Wed, Feb 13, 2013 at 10:21 AM, MORY, CYRIL wrote: > > Hi, > > > > > > > > I'm reinstalling ITK and RTK, and I was wondering which CMAKE > > options in ITK were recommended for the use of RTK. > > > > The wiki says to switch ITK_USE_REVIEW on, which I did, but it > > doesn't give any more advice. > > > > > > > > So here are my questions (some of which probably have nothing to do > > with RTK, sorry) : > > > > > > > > - What about the FFTW-related options ? RTK uses FFTW to > > ramp-filter the projections, right ? Should I activate the single > > precision or the double precision FFTW ? (I tried activating both, > > it lead to some kind of conflict and the linker couldn't find the > > libraries) > > > > - In order to be able to track an error in my RTK code and see > > where it crashes in ITK, do I need to compile ITK in Debug mode ? > > > > - Do you have recommendations about the BUILD_SHARED_LIBRARIES > > option (other than the simple difference between shared and static > > libraries) ? > > > > - Anything else ? > > > > > > > > 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 > > > > ________________________________ > 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 croow at yahoo.com Mon Feb 25 20:23:53 2013 From: croow at yahoo.com (M Miller) Date: Mon, 25 Feb 2013 17:23:53 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom Message-ID: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Tue Feb 26 03:36:49 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Tue, 26 Feb 2013 09:36:49 +0100 Subject: [Rtk-users] trouble projecting phantom In-Reply-To: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> References: <1361841833.26776.YahooMailClassic@web163806.mail.gq1.yahoo.com> Message-ID: Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > > Thanks > Micah > > _______________________________________________ > 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 croow at yahoo.com Wed Feb 27 00:45:48 2013 From: croow at yahoo.com (M Miller) Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) Subject: [Rtk-users] trouble projecting phantom In-Reply-To: Message-ID: <1361943948.94604.YahooMailClassic@web163804.mail.gq1.yahoo.com> Scaling the phantom worked perfectly. You mentioned that a reconstruction will need to specify the source outside of the volume. How can I specify that? What parameters would you pass to rtkfdk.exe to reconstruct the phantom? ? Thanks Micah --- On Tue, 2/26/13, Simon Rit wrote: From: Simon Rit Subject: Re: [Rtk-users] trouble projecting phantom To: "M Miller" Cc: rtk-users at openrtk.org Date: Tuesday, February 26, 2013, 12:36 AM Hi Micah, I have given it a try and I think I obtain the expected result if you use the SheppLogan file that we provide here http://midas3.kitware.com/midas/download?items=27326 However, the result might surprise you because your source is in the phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). You can scale the shepp logan phantom using the following command rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension 1024 --phantomscale 10 You will then obtain more meaningful results, i.e., the full phantom will be in the beam. Note by the way that if you use rtkfdk afterwards, you will have to be careful to have the source outside the volume as well. I have recently noticed that there was a bug when the source was in the volume, I will fix it as soon as possible. Simon On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: I've been unable to project a phantom, or anything else, at high magnification. Here's the steps I've think should work, but don't. ? "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 --sdd=870.86 --sid=65.93" ? These are the values from my actual CT system. Next I try using rtkprojectgeometricphantom to create some projections. ? "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha --spacing 1 --dimension 1024 --phantomfile SheppLogan.txt" ? Inspecting the output projections shows they're mostly unrecognizable. Repeating these steps with a higher SID does produce the expected phantom projections. I've had no luck using real data, so I thought I'd try a simple phantom, but it's turned out to be not so simple. ? Is RTK limited somehow with respect to magnification, or are my expectations unrealsitic? Am I missing a command-line switch? ? Thanks Micah _______________________________________________ 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 hdb1991a2012 at gmail.com Thu Feb 28 09:39:35 2013 From: hdb1991a2012 at gmail.com (=?GB2312?B?ucXUwg==?=) Date: Thu, 28 Feb 2013 22:39:35 +0800 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: Hi, I have a problem. how to read the .mha file? Can i use the matlab? Debin 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the source > outside of the volume. How can I specify that? What parameters would you > pass to rtkfdk.exe to reconstruct the phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result if you use > the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is in the > phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). > You can scale the shepp logan phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension > 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full phantom will > be in the beam. > Note by the way that if you use rtkfdk afterwards, you will have to be > careful to have the source outside the volume as well. I have recently > noticed that there was a bug when the source was in the volume, I will fix > it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: > > > > > > > I've been unable to project a phantom, or anything else, at high > magnification. Here's the steps I've think should work, but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 > --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try using > rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha > --spacing 1 --dimension 1024 --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly unrecognizable. > Repeating these steps with a higher SID does produce the expected phantom > projections. I've had no luck using real data, so I thought I'd try a > simple phantom, but it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are my > expectations unrealsitic? Am I missing a command-line switch? > ? > Thanks > Micah > _______________________________________________ > 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: < > http://public.kitware.com/pipermail/rtk-users/attachments/20130226/abec7e30/attachment-0001.htm > > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Feb 28 09:42:37 2013 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 28 Feb 2013 15:42:37 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: This is not a RTK question but an ITK question... mha is the file format of ITK. Many readers around, some are matlab: http://www.itk.org/pipermail/insight-users/2005-May/013134.html The difference between mha and mhd is that the second separates the data in two files, raw and header, not mha. Simon On Thu, Feb 28, 2013 at 3:39 PM, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 >> >> Send Rtk-users mailing list submissions to >> rtk-users at openrtk.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> or, via email, send a message with subject or body 'help' to >> rtk-users-request at openrtk.org >> >> You can reach the person managing the list at >> rtk-users-owner at openrtk.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Rtk-users digest..." >> >> >> Today's Topics: >> >> 1. Re: trouble projecting phantom (M Miller) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) >> From: M Miller >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: Simon Rit >> Cc: rtk-users at openrtk.org >> Message-ID: >> <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Scaling the phantom worked perfectly. >> You mentioned that a reconstruction will need to specify the source >> outside of the volume. How can I specify that? What parameters would you >> pass to rtkfdk.exe to reconstruct the phantom? >> ? >> Thanks >> Micah >> >> --- On Tue, 2/26/13, Simon Rit wrote: >> >> >> From: Simon Rit >> Subject: Re: [Rtk-users] trouble projecting phantom >> To: "M Miller" >> Cc: rtk-users at openrtk.org >> Date: Tuesday, February 26, 2013, 12:36 AM >> >> >> Hi Micah, >> I have given it a try and I think I obtain the expected result if you use >> the SheppLogan file that we provide here >> http://midas3.kitware.com/midas/download?items=27326 >> However, the result might surprise you because your source is in the >> phantom (sid=65.93 vs largest ellipsoid which is A=88.32 B=115.2 C=117.76). >> You can scale the shepp logan phantom using the following command >> rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 --dimension >> 1024 --phantomscale 10 >> You will then obtain more meaningful results, i.e., the full phantom will >> be in the beam. >> Note by the way that if you use rtkfdk afterwards, you will have to be >> careful to have the source outside the volume as well. I have recently >> noticed that there was a bug when the source was in the volume, I will fix >> it as soon as possible. >> Simon >> >> >> On Tue, Feb 26, 2013 at 2:23 AM, M Miller wrote: >> >> >> >> >> >> >> I've been unable to project a phantom, or anything else, at high >> magnification. Here's the steps I've think should work, but don't. >> ? >> "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 --arc=360 >> --sdd=870.86 --sid=65.93" >> ? >> These are the values from my actual CT system. Next I try using >> rtkprojectgeometricphantom to create some projections. >> ? >> "rtkprojectgeometricphantom -g geo.xml -o projs\projections1024.mha >> --spacing 1 --dimension 1024 --phantomfile >> SheppLogan.txt" >> ? >> Inspecting the output projections shows they're mostly unrecognizable. >> Repeating these steps with a higher SID does produce the expected phantom >> projections. I've had no luck using real data, so I thought I'd try a simple >> phantom, but it's turned out to be not so simple. >> ? >> Is RTK limited somehow with respect to magnification, or are my >> expectations unrealsitic? Am I missing a command-line switch? >> ? >> Thanks >> Micah >> _______________________________________________ >> 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: >> >> >> ------------------------------ >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users >> >> >> End of Rtk-users Digest, Vol 6, Issue 6 >> *************************************** > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From marc.vila-oliva at creatis.insa-lyon.fr Thu Feb 28 09:50:12 2013 From: marc.vila-oliva at creatis.insa-lyon.fr (Marc Vila Oliva) Date: Thu, 28 Feb 2013 15:50:12 +0100 Subject: [Rtk-users] Rtk-users Digest, Vol 6, Issue 6 In-Reply-To: References: Message-ID: <1362063013.21807.5.camel@mvila-laptop> Hello Debin, You can read a .mha file with "VV" for instance. It can be easily downloaded at: http://www.creatis.insa-lyon.fr/rio/vv/ With Matlab I am not pretty sure but as you don't have directly the raw file of your image. You have to take into account the header of your file and then you will be able to read your image. Or maybe there is already a toolbox which does this for you in Matlab. If you can decide the format of your file I would recommend you to use .mhd extension, in that case you would have your header in a separate file (.mhd) and your raw image (.raw). I hope it helps! Cheers, Marc On Thu, 2013-02-28 at 22:39 +0800, ?? wrote: > Hi, > I have a problem. how to read the .mha file? Can i use the matlab? > Debin > > 2013/2/28 > Send Rtk-users mailing list submissions to > rtk-users at openrtk.org > > To subscribe or unsubscribe via the World Wide Web, visit > > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > or, via email, send a message with subject or body 'help' to > rtk-users-request at openrtk.org > > You can reach the person managing the list at > rtk-users-owner at openrtk.org > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of Rtk-users digest..." > > > Today's Topics: > > 1. Re: trouble projecting phantom (M Miller) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Feb 2013 21:45:48 -0800 (PST) > From: M Miller > Subject: Re: [Rtk-users] trouble projecting phantom > To: Simon Rit > Cc: rtk-users at openrtk.org > Message-ID: > > <1361943948.94604.YahooMailClassic at web163804.mail.gq1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Scaling the phantom worked perfectly. > You mentioned that a reconstruction will need to specify the > source outside of the volume. How can I specify that? What > parameters would you pass to rtkfdk.exe to reconstruct the > phantom? > ? > Thanks > Micah > > --- On Tue, 2/26/13, Simon Rit > wrote: > > > From: Simon Rit > Subject: Re: [Rtk-users] trouble projecting phantom > To: "M Miller" > Cc: rtk-users at openrtk.org > Date: Tuesday, February 26, 2013, 12:36 AM > > > Hi Micah, > I have given it a try and I think I obtain the expected result > if you use the SheppLogan file that we provide here > http://midas3.kitware.com/midas/download?items=27326 > However, the result might surprise you because your source is > in the phantom (sid=65.93 vs largest ellipsoid which is > A=88.32 B=115.2 C=117.76). You can scale the shepp logan > phantom using the following command > rtkprojectshepploganphantom -g geo.xml -o proj.mha --spacing 1 > --dimension 1024 --phantomscale 10 > You will then obtain more meaningful results, i.e., the full > phantom will be in the beam. > Note by the way that if you use rtkfdk afterwards, you will > have to be careful to have the source outside the volume as > well. I have recently noticed that there was a bug when the > source was in the volume, I will fix it as soon as possible. > Simon > > > On Tue, Feb 26, 2013 at 2:23 AM, M Miller > wrote: > > > > > > > I've been unable to project a phantom, or anything else, at > high magnification. Here's the steps I've think should work, > but don't. > ? > "rtksimulatedgeometry.exe --output=geo.xml --nproj=1600 > --arc=360 --sdd=870.86 --sid=65.93" > ? > These are the values from my actual CT system. Next I try > using rtkprojectgeometricphantom to create some projections. > ? > "rtkprojectgeometricphantom -g geo.xml -o projs > \projections1024.mha --spacing 1 --dimension 1024 > --phantomfile > SheppLogan.txt" > ? > Inspecting the output projections shows they're mostly > unrecognizable. Repeating these steps with a higher SID does > produce the expected phantom projections. I've had no luck > using real data, so I thought I'd try a simple phantom, but > it's turned out to be not so simple. > ? > Is RTK limited somehow with respect to magnification, or are > my expectations unrealsitic? Am I missing a command-line > switch? > ? > Thanks > Micah > _______________________________________________ > 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: > > > ------------------------------ > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > End of Rtk-users Digest, Vol 6, Issue 6 > *************************************** > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users