From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 53021 bytes Desc: not available URL: From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 53021 bytes Desc: not available URL: From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 53021 bytes Desc: not available URL: From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 53021 bytes Desc: not available URL: From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 53021 bytes Desc: not available URL: From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 53021 bytes Desc: not available URL: From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 53021 bytes Desc: not available URL: From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 53021 bytes Desc: not available URL: From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 53021 bytes Desc: not available URL: From taylor at braun-jones.org Mon Jun 2 22:52:32 2014 From: taylor at braun-jones.org (Taylor Braun-Jones) Date: Mon, 2 Jun 2014 22:52:32 -0400 Subject: [Rtk-users] Python bindings for RTK Message-ID: Hello rtk-users, The complexity of C++ significantly raises the barrier to entry for those that would like to experiment with the reconstruction algorithms of RTK. Does RTK have (or plan to have) python bindings available? (something like SimpleITK) With the 1.0 release out (congrats!), maybe this is the right time to look at this? If someone were to get the effort started with a build framework and wrapping a couple filters as examples, I'd be willing to help out with some of the wrapping work. Thanks, Taylor -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.jomier at kitware.com Tue Jun 3 01:27:02 2014 From: julien.jomier at kitware.com (Julien Jomier) Date: Tue, 03 Jun 2014 07:27:02 +0200 Subject: [Rtk-users] Python bindings for RTK In-Reply-To: References: Message-ID: <538D5CA6.7080306@kitware.com> Taylor, This is a very good point. We have already started this effort with bindings of RTK similar to SimpleITK. We have no estimated date at this point, but hopefully some time in the Fall. Julien On 03/06/2014 04:52, Taylor Braun-Jones wrote: > Hello rtk-users, > > The complexity of C++ significantly raises the barrier to entry for > those that would like to experiment with the reconstruction algorithms > of RTK. Does RTK have (or plan to have) python bindings available? > (something like SimpleITK) With the 1.0 release out (congrats!), maybe > this is the right time to look at this? > > If someone were to get the effort started with a build framework and > wrapping a couple filters as examples, I'd be willing to help out with > some of the wrapping work. > > Thanks, > Taylor > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > From Uffe.Bernchou at rsyd.dk Tue Jun 3 08:36:48 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 12:36:48 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Tue Jun 3 11:46:23 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Tue, 3 Jun 2014 15:46:23 +0000 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Hi Cyril, That's great. Thank you very much. Best Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cyril.mory at creatis.insa-lyon.fr Tue Jun 3 11:30:09 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Tue, 03 Jun 2014 17:30:09 +0200 Subject: [Rtk-users] Release of RTK v1.0.0 In-Reply-To: References: Message-ID: <538DEA01.4070404@creatis.insa-lyon.fr> Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > > Dear Simon, > > Do you have a reference publication for the new iterative 3D > reconstruction with 3D TV regularization implemented in the v.1.00 > release of RTK? > > Best regards, > > Uffe > > ------------------------------ > > Uffe Bernchou, Ph.D. > > Postdoc > > Laboratory of Radiation Physics, Odense University Hospital > > Institute of Clinical Research, University of Southern Denmark > > Email: uffe.bernchou at rsyd.dk > > Phone: +45 29796478 > > Sdr. Boulevard 29, Indgang 97, 5000 Odense C > > ------------------------------------------------------------------------ > > *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af > *Simon Rit > *Sendt:* 28. april 2014 16:33 > *Til:* rtk-users at openrtk.org > *Emne:* [Rtk-users] Release of RTK v1.0.0 > > Dear RTK users, > > It is my pleasure to announce the release of RTK v1.0.0. As announced > previously on the mailing list, the new release is no more compatible > with ITK 3.20, this release is compatible with ITK v4.2.0 and more > recent releases. We are still actively developing RTK with both new > filtered backprojection and iterative algorithms so I still encourage > the use of git to be up-to-date. As usual, please report any issue > that you encounter with RTK, we are happy to help when we can. Note > the list of publications using RTK > on the main > site: please send me the DOI of your articles if you want them to > appear there. We have also added a webpage with use cases > . > > I'm looking forward to your feedback. Regards, > > Simon > > > Release notes: > > - introduction of the itk::CudaImage object that better handles the > memory transfers between the CPU and the GPU > > - pre-processing for projection images: binning, median filter, > lookup-table filter > > - filtered backprojection with offset center-of-rotation based on > [Gullberg et al, TMI, 1986] > > - improved Joseph forward projector and implementation of its exact > adjoint > > - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] > - new iterative 3D reconstruction using conjugate gradient optimization > > - new iterative 3D reconstruction with 3D TV regularization using the > Alternating Direction Method of Multipliers combined with the > Augmented Lagrangian method > > Documentation: > > - improved Doxygen with dot graphs to describe mini-pipelines, e.g., > in the SART page > > > - updated consortium > and alternative > platforms pages > > - updated wiki > > > > _______________________________________________ > Rtk-users mailing list > Rtk-users at openrtk.org > http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Thu Jun 19 05:02:55 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Thu, 19 Jun 2014 09:02:55 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <538DEA01.4070404@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TVresultScreenDump.png Type: image/png Size: 275900 bytes Desc: TVresultScreenDump.png URL: From cyril.mory at creatis.insa-lyon.fr Thu Jun 19 05:32:14 2014 From: cyril.mory at creatis.insa-lyon.fr (Cyril Mory) Date: Thu, 19 Jun 2014 11:32:14 +0200 Subject: [Rtk-users] 3D TV regularization In-Reply-To: References: <538DEA01.4070404@creatis.insa-lyon.fr> Message-ID: <53A2AE1E.1060007@creatis.insa-lyon.fr> Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: > > Dear Cyril, > > We are currently playing with the 3D TV regularization iterative > reconstruction implemented in RTK for our cone beam data. The results > look promising indeed. > > One thing that worries me a little is a ring artefact we observe in > the reconstructions (please see attached image). This ring artefact we > usually remove in the standard fdk reconstruction by using padding. > Does the TV regularization iterative reconstruction have a similar > feature for removing the ring artefact? > > Best regards > > Uffe Bernchou > > ------------------------------------------------------------------------ > > *Fra:*Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] > *Sendt:* 3. juni 2014 17:30 > *Til:* Uffe Bernchou; 'Simon Rit' > *Cc:* rtk-users at openrtk.org > *Emne:* Re: [Rtk-users] Release of RTK v1.0.0 > > Dear Uffe, > > The method is described and compared to others in this PhD thesis : > http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf > That's for the pdf. You can access the description here : > http://tel.archives-ouvertes.fr/tel-00985728 > > Your comments/questions are welcome. > > Best regards, > Cyril > > Le 03/06/2014 14:36, Uffe Bernchou a ?crit : > >> Dear Simon, >> >> Do you have a reference publication for the new iterative 3D >> reconstruction with 3D TV regularization implemented in the v.1.00 >> release of RTK? >> >> Best regards, >> >> Uffe >> >> ------------------------------ >> >> Uffe Bernchou, Ph.D. >> >> Postdoc >> >> Laboratory of Radiation Physics, Odense University Hospital >> >> Institute of Clinical Research, University of Southern Denmark >> >> Email: uffe.bernchou at rsyd.dk >> >> Phone: +45 29796478 >> >> Sdr. Boulevard 29, Indgang 97, 5000 Odense C >> >> ------------------------------------------------------------------------ >> >> *Fra:*Rtk-users [mailto:rtk-users-bounces at openrtk.org] *P? vegne af >> *Simon Rit >> *Sendt:* 28. april 2014 16:33 >> *Til:* rtk-users at openrtk.org >> *Emne:* [Rtk-users] Release of RTK v1.0.0 >> >> Dear RTK users, >> >> It is my pleasure to announce the release of RTK v1.0.0. As announced >> previously on the mailing list, the new release is no more compatible >> with ITK 3.20, this release is compatible with ITK v4.2.0 and more >> recent releases. We are still actively developing RTK with both new >> filtered backprojection and iterative algorithms so I still encourage >> the use of git to be up-to-date. As usual, please report any issue >> that you encounter with RTK, we are happy to help when we can. Note >> the list of publications using RTK >> on the main >> site: please send me the DOI of your articles if you want them to >> appear there. We have also added a webpage with use cases >> . >> >> I'm looking forward to your feedback. Regards, >> >> Simon >> >> >> Release notes: >> >> - introduction of the itk::CudaImage object that better handles the >> memory transfers between the CPU and the GPU >> >> - pre-processing for projection images: binning, median filter, >> lookup-table filter >> >> - filtered backprojection with offset center-of-rotation based on >> [Gullberg et al, TMI, 1986] >> >> - improved Joseph forward projector and implementation of its exact >> adjoint >> >> - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] >> - new iterative 3D reconstruction using conjugate gradient optimization >> >> - new iterative 3D reconstruction with 3D TV regularization using the >> Alternating Direction Method of Multipliers combined with the >> Augmented Lagrangian method >> >> Documentation: >> >> - improved Doxygen with dot graphs to describe mini-pipelines, e.g., >> in the SART page >> >> >> - updated consortium >> and alternative >> platforms pages >> >> - updated wiki >> >> >> >> >> _______________________________________________ >> Rtk-users mailing list >> Rtk-users at openrtk.org >> http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users > > > > -- > Cyril Mory, Post-doc > CREATIS > Leon Berard cancer treatment center > 28 rue La?nnec > 69373 Lyon cedex 08 FRANCE > > Mobile: +33 6 69 46 73 79 > > ------------------------------------------------------------------------ > > > > > > Ce courrier ?lectronique ne contient aucun virus ou logiciel > malveillant parce que la protection Antivirus avast! > est active. > -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Uffe.Bernchou at rsyd.dk Fri Jun 20 04:46:30 2014 From: Uffe.Bernchou at rsyd.dk (Uffe Bernchou) Date: Fri, 20 Jun 2014 08:46:30 +0000 Subject: [Rtk-users] 3D TV regularization In-Reply-To: <53A2AE1E.1060007@creatis.insa-lyon.fr> References: <538DEA01.4070404@creatis.insa-lyon.fr> <53A2AE1E.1060007@creatis.insa-lyon.fr> Message-ID: Thank you very much. That seems to do the trick. Best, Uffe ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 19. juni 2014 11:32 Til: Uffe Bernchou Cc: rtk-users at openrtk.org Emne: Re: 3D TV regularization Dear Uffe, Simply increasing the size of the reconstructed volume until the object is fully contained in it should do the trick. An intuitive way to understand this is the following: the algorithm tries to "explain" the attenuation it sees on the projections. If the data has been partially truncated, some rays have "extra attenuation" that has to go somewhere in the reconstructed volume. The center of the reconstructed volume is constrained by all the other rays, so this "extra attenuation" is pushed to the borders. If, on the other hand, the reconstructed volume is large enough, this "extra attenuation" can go where it belongs, and does not cause hyperattenuation on the borders. Note that you can still apply a crop to FOV at the very end of the reconstruction process. I hope it helps Regards, Cyril On 06/19/2014 11:02 AM, Uffe Bernchou wrote: Dear Cyril, We are currently playing with the 3D TV regularization iterative reconstruction implemented in RTK for our cone beam data. The results look promising indeed. One thing that worries me a little is a ring artefact we observe in the reconstructions (please see attached image). This ring artefact we usually remove in the standard fdk reconstruction by using padding. Does the TV regularization iterative reconstruction have a similar feature for removing the ring artefact? Best regards Uffe Bernchou ________________________________ Fra: Cyril Mory [mailto:cyril.mory at creatis.insa-lyon.fr] Sendt: 3. juni 2014 17:30 Til: Uffe Bernchou; 'Simon Rit' Cc: rtk-users at openrtk.org Emne: Re: [Rtk-users] Release of RTK v1.0.0 Dear Uffe, The method is described and compared to others in this PhD thesis : http://tel.archives-ouvertes.fr/docs/00/98/57/28/PDF/TH2014_Mory_Cyril.pdf That's for the pdf. You can access the description here : http://tel.archives-ouvertes.fr/tel-00985728 Your comments/questions are welcome. Best regards, Cyril Le 03/06/2014 14:36, Uffe Bernchou a ?crit : Dear Simon, Do you have a reference publication for the new iterative 3D reconstruction with 3D TV regularization implemented in the v.1.00 release of RTK? Best regards, Uffe ------------------------------ Uffe Bernchou, Ph.D. Postdoc Laboratory of Radiation Physics, Odense University Hospital Institute of Clinical Research, University of Southern Denmark Email: uffe.bernchou at rsyd.dk Phone: +45 29796478 Sdr. Boulevard 29, Indgang 97, 5000 Odense C ________________________________ Fra: Rtk-users [mailto:rtk-users-bounces at openrtk.org] P? vegne af Simon Rit Sendt: 28. april 2014 16:33 Til: rtk-users at openrtk.org Emne: [Rtk-users] Release of RTK v1.0.0 Dear RTK users, It is my pleasure to announce the release of RTK v1.0.0. As announced previously on the mailing list, the new release is no more compatible with ITK 3.20, this release is compatible with ITK v4.2.0 and more recent releases. We are still actively developing RTK with both new filtered backprojection and iterative algorithms so I still encourage the use of git to be up-to-date. As usual, please report any issue that you encounter with RTK, we are happy to help when we can. Note the list of publications using RTK on the main site: please send me the DOI of your articles if you want them to appear there. We have also added a webpage with use cases. I'm looking forward to your feedback. Regards, Simon Release notes: - introduction of the itk::CudaImage object that better handles the memory transfers between the CPU and the GPU - pre-processing for projection images: binning, median filter, lookup-table filter - filtered backprojection with offset center-of-rotation based on [Gullberg et al, TMI, 1986] - improved Joseph forward projector and implementation of its exact adjoint - improved SART reconstruction [Andersen, Ultrason Imaging, 1984] - new iterative 3D reconstruction using conjugate gradient optimization - new iterative 3D reconstruction with 3D TV regularization using the Alternating Direction Method of Multipliers combined with the Augmented Lagrangian method Documentation: - improved Doxygen with dot graphs to describe mini-pipelines, e.g., in the SART page - updated consortium and alternative platforms pages - updated wiki _______________________________________________ Rtk-users mailing list Rtk-users at openrtk.org http://public.kitware.com/cgi-bin/mailman/listinfo/rtk-users -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 ________________________________ [http://static.avast.com/emails/avast-mail-stamp.png] Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection Antivirus avast! est active. -- -- Cyril Mory, Post-doc CREATIS Leon Berard cancer treatment center 28 rue La?nnec 69373 Lyon cedex 08 FRANCE Mobile: +33 6 69 46 73 79 -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsieandy at gmail.com Sun Jun 22 10:22:47 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 00:22:47 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK Message-ID: Hi Simon & RTK developers/users, I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 (with Win 8.1 x64, compiled using Visual Studio 2012). I have installed the latest cuda toolkit (v6.0), and has confirmed that it worked properly using the samples in the cuda toolkit as well as MATLAB. I have also successfully compiled RTK with cuda found. However, when I tried to execute cuda applications such as rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime errors: For rtkbackprojections: ====================== ExceptionObject caught with bp->Update() itk::ExceptionObject (000000698148F5E8) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtkfdk: ====================== ExceptionObject caught with writer->Update() itk::ExceptionObject (0000004AF047E8E0) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu Line: 139 Description: itk::ERROR: CUDA ERROR: invalid device function ====================== For rtksart: ====================== ExceptionObject caught with sart->Update() itk::ExceptionObject (00000086AE63F050) Location: "unknown" File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu Line: 251 Description: itk::ERROR: CUDA ERROR: invalid texture reference ====================== These errors were all caught by "CUDA_CHECK_ERROR". Do you know what might be the problem here? I also tried these with a down-sampled projection sets with only 10 projections, so it seems that this is not a memory shortage issue. It is also worth mentioning that everything works properly on another computer with a NVIDIA Quadro 4000. Any clue would be of great help. Thanks! Cheers, Andy -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Sun Jun 22 17:44:28 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Sun, 22 Jun 2014 23:44:28 +0200 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Andy, I'm not sure... Can you try disabling some archtiecture specific options in cmake/FindCUDA_wrap.cmake? In this file, you can try commenting lines 62 to 74. Simon On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > Hi Simon & RTK developers/users, > > I'm trying to get the cuda applications in RTK to work on my NVIDIA GTX770 > (with Win 8.1 x64, compiled using Visual Studio 2012). > I have installed the latest cuda toolkit (v6.0), and has confirmed that it > worked properly using the samples in the cuda toolkit as well as MATLAB. > I have also successfully compiled RTK with cuda found. > However, when I tried to execute cuda applications such as > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > errors: > > For rtkbackprojections: > ====================== > ExceptionObject caught with bp->Update() > > itk::ExceptionObject (000000698148F5E8) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtkfdk: > ====================== > ExceptionObject caught with writer->Update() > > itk::ExceptionObject (0000004AF047E8E0) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > Line: 139 > Description: itk::ERROR: CUDA ERROR: invalid device function > ====================== > > For rtksart: > ====================== > ExceptionObject caught with sart->Update() > > itk::ExceptionObject (00000086AE63F050) > Location: "unknown" > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > Line: 251 > Description: itk::ERROR: CUDA ERROR: invalid texture reference > ====================== > > > These errors were all caught by "CUDA_CHECK_ERROR". > Do you know what might be the problem here? > I also tried these with a down-sampled projection sets with only 10 > projections, so it seems that this is not a memory shortage issue. > > It is also worth mentioning that everything works properly on another > computer with a NVIDIA Quadro 4000. > > Any clue would be of great help. Thanks! > > Cheers, > Andy > > _______________________________________________ > Rtk-users mailing list > Rtk-users at public.kitware.com > http://public.kitware.com/mailman/listinfo/rtk-users > From hsieandy at gmail.com Mon Jun 23 04:27:48 2014 From: hsieandy at gmail.com (Andy Shieh) Date: Mon, 23 Jun 2014 18:27:48 +1000 Subject: [Rtk-users] "Invalid device function" when using cuda applications in RTK In-Reply-To: References: Message-ID: Hi Simon, Thank you so so much - that actually solved the problem. I realized it could be because I was using an older version of RTK, in which the FindCUDA_wrap.cmake file did not include "-gencode arch=compute_30,code=sm_30" (my gpu compute compatibility is 3.0), and disabling that probably allows the compiler to automatically determine the correct architecture setting. I really should have tried with the updated RTK version earlier, in which compute_30 was specified in the cmake file. Anyways, thank you!!! Cheers, Andy 2014-06-23 7:44 GMT+10:00 Simon Rit : > Hi Andy, > I'm not sure... Can you try disabling some archtiecture specific > options in cmake/FindCUDA_wrap.cmake? In this file, you can try > commenting lines 62 to 74. > Simon > > On Sun, Jun 22, 2014 at 4:22 PM, Andy Shieh wrote: > > Hi Simon & RTK developers/users, > > > > I'm trying to get the cuda applications in RTK to work on my NVIDIA > GTX770 > > (with Win 8.1 x64, compiled using Visual Studio 2012). > > I have installed the latest cuda toolkit (v6.0), and has confirmed that > it > > worked properly using the samples in the cuda toolkit as well as MATLAB. > > I have also successfully compiled RTK with cuda found. > > However, when I tried to execute cuda applications such as > > rtkbackprojections, rtkfdk, rtksart, I kept getting the following runtime > > errors: > > > > For rtkbackprojections: > > ====================== > > ExceptionObject caught with bp->Update() > > > > itk::ExceptionObject (000000698148F5E8) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaBackProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtkfdk: > > ====================== > > ExceptionObject caught with writer->Update() > > > > itk::ExceptionObject (0000004AF047E8E0) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaFFTRampImageFilter.cu > > Line: 139 > > Description: itk::ERROR: CUDA ERROR: invalid device function > > ====================== > > > > For rtksart: > > ====================== > > ExceptionObject caught with sart->Update() > > > > itk::ExceptionObject (00000086AE63F050) > > Location: "unknown" > > File: D:/SourceCode/RTK_Andy/code/rtkCudaForwardProjectionImageFilter.cu > > Line: 251 > > Description: itk::ERROR: CUDA ERROR: invalid texture reference > > ====================== > > > > > > These errors were all caught by "CUDA_CHECK_ERROR". > > Do you know what might be the problem here? > > I also tried these with a down-sampled projection sets with only 10 > > projections, so it seems that this is not a memory shortage issue. > > > > It is also worth mentioning that everything works properly on another > > computer with a NVIDIA Quadro 4000. > > > > Any clue would be of great help. Thanks! > > > > Cheers, > > Andy > > > > _______________________________________________ > > Rtk-users mailing list > > Rtk-users at public.kitware.com > > http://public.kitware.com/mailman/listinfo/rtk-users > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Thu Jun 26 13:56:21 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Thu, 26 Jun 2014 19:56:21 +0200 Subject: [Rtk-users] The question of RTK In-Reply-To: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> Message-ID: Please use the mailing list for user questions. The general description of the steps is adressed on the wiki. If you encounter a compilation problem, report the error on the mailing list and we'll do our best to help you. Simon On Thu, Jun 26, 2014 at 9:28 AM, xiaody wrote: > Dir Simon Rit: > > I set up RTK with Ubuntu 12.02 in vmare workstation. I have built ITK and > RTK with some errors because there is no cuda. I want to do Step 3 ? > Running the HelloWorld application. But I don?t know how to do. > > How could I do the following step? > > ? Run CMake on the HelloWorld directory and create a HelloWorld-bin > > ? Configure and build the project using your favorite compiler > > ? Run the HelloWorld application. If everything runs correctly you > should see "RTK Hello World!" written on the console > > > > > > Dayu Xiao > > Northeastern University, China. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simon.rit at creatis.insa-lyon.fr Fri Jun 27 10:56:32 2014 From: simon.rit at creatis.insa-lyon.fr (Simon Rit) Date: Fri, 27 Jun 2014 16:56:32 +0200 Subject: [Rtk-users] =?utf-8?b?562U5aSNOiBUaGUgcXVlc3Rpb24gb2YgUlRL?= In-Reply-To: <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> References: <000c01cf9110$39eecf90$adcc6eb0$@bmie.neu.edu.cn> <001501cf91b6$298d8690$7ca893b0$@bmie.neu.edu.cn> Message-ID: Ok so this is the last reminder to use the RTK mailing list, next time I won't answer a personal email. Moreover, please report the compilation outputs using text, not with useless snapshots. I don't have the cmake_minimum_required warning when I compile the HelloWorld example. Are you sure that the ../HelloWorld directory contains this file ? Simon On Fri, Jun 27, 2014 at 5:16 AM, xiaody wrote: > *Dir:* > > * I press [g].* > > > > Dayu Xiao > > Northeastern University, China. > > > -------------- next part -------------- An HTML attachment was scrubbed... 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