Hi, Congratulations on this code translation. Only 17 cycles according to your phase.txt file is very few. But there seems to be something else going one. I would suggest to remove the parker weights because RTK might detect a short scan since you have large gaps between projections in the same cycle. Or set the angular threshold <http://www.openrtk.org/Doxygen/classrtk_1_1ParkerShortScanImageFilter.html#a7f0bc650a54b022cb47523841749d741> to a larger value to be sure that it does not apply any such weight, the default is pi/9 and not large enough in your case. Simon
On Thu, May 14, 2020 at 11:58 PM Zhang, Zhehao <[email protected]> wrote: > Hi, > > Sorry for my fault, I think I have made that link public this time. The > results are also uploaded. > > The attachment is my phase-correlated reconstruction result (the first > phase of total five phases). Thank you. > > BTW, if I need to utilize more projections for each phase, is there some > integrated method in RTK to do so? Or you mean that I need to handle it by > myself? > > > > Best regards, > > Zhehao > > *From: *Simon Rit <[email protected]> > *Sent: *Thursday, May 14, 2020 2:17 AM > *To: *Zhang, Zhehao <[email protected]> > *Cc: *[email protected] > *Subject: *Re: [Rtk-users] 4D Phase-correlated Reconstruction > > > > Hi, > > Yes, you understood correctly. Adding projections will not fix the problem > of angular gaps but will add some motion blur. This is, in my experience, > the best way to proceed but you're free to do otherwise. > > I can't access your link, it seems to be protected. Can you provide just > one snapshot of your result? > > Simon > > > > On Thu, May 14, 2020 at 8:13 AM Zhang, Zhehao <[email protected]> > wrote: > > Hi, > > > > First, thank you for your reply. I am following the rtkfourdfdk to do the > phase-correlated recon now. However, the result is not desirable and I am > wondering whether the bad results result from too few projections for each > phase. > > If I understand the rtk::SelectOneProjectionPerCycleImageFilter correctly, > it only select one projection from per respiratory cycle for each phase. So > if 20 projections were acquired per respiratory cycle and I want to > reconstruct 10 phases, only half projections will be used, right? I don’t > know why we abandon some projections and is there some way I can use all > the data? That’s to say, select 2 projections for each one of total 10 > phases per respiratory cycle. > > I also put my Python code and used data here( > https://drive.google.com/drive/folders/1SFXr4ehI1N8Wh0BAMlRqIah9cXwukRYJ ). > > > > > Thank you again. > > Zhehao > > > > > > *From: *Simon Rit <[email protected]> > *Sent: *Wednesday, May 13, 2020 3:59 AM > *To: *Zhang, Zhehao <[email protected]> > *Cc: *[email protected] > *Subject: *Re: [Rtk-users] 4D Phase-correlated Reconstruction > > > > Hi, > > I think you should look at rtkfourdfdk > <https://github.com/SimonRit/RTK/blob/master/applications/rtkfourdfdk/rtkfourdfdk.cxx> > which does what you want. rtk::SelectOneProjectionPerCycleImageFilter will > select the projections for you. Can you try to reimplement this in Python? > We'll help if you're stuck but this is the right file to use as a basis for > your dev. > > Simon > > > > On Wed, May 13, 2020 at 8:07 AM Zhang, Zhehao <[email protected]> > wrote: > > > > Dear all, > > > > I am trying to do the 4D phase-correlated CBCT reconstruction under Python > environment. What I have are the projection data(.mha), geometry info(.xml) > and the repiratory info(.txt). You can check the attachment for the phase > file. I want just to simply ‘divide’ the projections and geometry into > different bins according to the phase information and perform FDK recon > separately, to get several different 3D images with streaks artifacts of > course. The Rooster is not necessary for me. > > > > I have spent lot of time on the given ‘4DROOSTERReconstruction’ example. I > think it used the ReorderProjectionsImageFilter order to do the separation. > However, I am stuck on how to perform it for Python since I didn’t figure > out how to read the phase.txt. Could you please give me some hints and is > it correct to call this order to achieve my goals? > > > > Additionally, I also saw another test example( > https://github.com/SimonRit/RTK/blob/master/test/rtkwarpprojectionstacktofourdtest.cxx) > which seems using ‘PhasesToInterpolationWeights’ , > ‘BackProjectionImageFilter’ and ‘DivideImageFilter ‘ to do this. I am > confused I should follow which way. And I also want to make sure why here > using BackProjectionImageFilter rather than FDKConeBeamReconstructionFilter. > > > > Sorry for these cumbersome questions. Really hope to get some help, which > means a lot for me. Thank you very much. > > > > Sincerely, > > Zhehao > > > > _______________________________________________ > Rtk-users mailing list > [email protected] > https://public.kitware.com/mailman/listinfo/rtk-users > > > > > > *From: *Zhang, Zhehao <[email protected]> > *Sent: *Thursday, May 14, 2020 2:38 AM > *To: *Simon Rit <[email protected]> > *Cc: *[email protected] > *Subject: *RE: [Rtk-users] 4D Phase-correlated Reconstruction > > > > Sorry for my fault, I think I have made that link public this time. The > results are also there. > > I attached two results, the better one is conventional FDK where also > projections are used (no separate phase) and another one is > phase-correlated recon (the shown is the first of five phases). > > BTW, if I need to utilize more projections for each phase, is there some > integrated method in RTK to do so? Or you mean that I need to handle it by > myself? > > > > Best regards, > > Zhehao > > *From: *Simon Rit <[email protected]> > *Sent: *Thursday, May 14, 2020 2:17 AM > *To: *Zhang, Zhehao <[email protected]> > *Cc: *[email protected] > *Subject: *Re: [Rtk-users] 4D Phase-correlated Reconstruction > > > > Hi, > > Yes, you understood correctly. Adding projections will not fix the problem > of angular gaps but will add some motion blur. This is, in my experience, > the best way to proceed but you're free to do otherwise. > > I can't access your link, it seems to be protected. Can you provide just > one snapshot of your result? > > Simon > > > > On Thu, May 14, 2020 at 8:13 AM Zhang, Zhehao <[email protected]> > wrote: > > Hi, > > > > First, thank you for your reply. I am following the rtkfourdfdk to do the > phase-correlated recon now. However, the result is not desirable and I am > wondering whether the bad results result from too few projections for each > phase. > > If I understand the rtk::SelectOneProjectionPerCycleImageFilter correctly, > it only select one projection from per respiratory cycle for each phase. So > if 20 projections were acquired per respiratory cycle and I want to > reconstruct 10 phases, only half projections will be used, right? I don’t > know why we abandon some projections and is there some way I can use all > the data? That’s to say, select 2 projections for each one of total 10 > phases per respiratory cycle. > > I also put my Python code and used data here( > https://drive.google.com/drive/folders/1SFXr4ehI1N8Wh0BAMlRqIah9cXwukRYJ ). > > > > > Thank you again. > > Zhehao > > > > > > *From: *Simon Rit <[email protected]> > *Sent: *Wednesday, May 13, 2020 3:59 AM > *To: *Zhang, Zhehao <[email protected]> > *Cc: *[email protected] > *Subject: *Re: [Rtk-users] 4D Phase-correlated Reconstruction > > > > Hi, > > I think you should look at rtkfourdfdk > <https://github.com/SimonRit/RTK/blob/master/applications/rtkfourdfdk/rtkfourdfdk.cxx> > which does what you want. rtk::SelectOneProjectionPerCycleImageFilter will > select the projections for you. Can you try to reimplement this in Python? > We'll help if you're stuck but this is the right file to use as a basis for > your dev. > > Simon > > > > On Wed, May 13, 2020 at 8:07 AM Zhang, Zhehao <[email protected]> > wrote: > > > > Dear all, > > > > I am trying to do the 4D phase-correlated CBCT reconstruction under Python > environment. What I have are the projection data(.mha), geometry info(.xml) > and the repiratory info(.txt). You can check the attachment for the phase > file. I want just to simply ‘divide’ the projections and geometry into > different bins according to the phase information and perform FDK recon > separately, to get several different 3D images with streaks artifacts of > course. The Rooster is not necessary for me. > > > > I have spent lot of time on the given ‘4DROOSTERReconstruction’ example. I > think it used the ReorderProjectionsImageFilter order to do the separation. > However, I am stuck on how to perform it for Python since I didn’t figure > out how to read the phase.txt. Could you please give me some hints and is > it correct to call this order to achieve my goals? > > > > Additionally, I also saw another test example( > https://github.com/SimonRit/RTK/blob/master/test/rtkwarpprojectionstacktofourdtest.cxx) > which seems using ‘PhasesToInterpolationWeights’ , > ‘BackProjectionImageFilter’ and ‘DivideImageFilter ‘ to do this. I am > confused I should follow which way. And I also want to make sure why here > using BackProjectionImageFilter rather than FDKConeBeamReconstructionFilter. > > > > Sorry for these cumbersome questions. Really hope to get some help, which > means a lot for me. Thank you very much. > > > > Sincerely, > > Zhehao > > > > _______________________________________________ > Rtk-users mailing list > [email protected] > https://public.kitware.com/mailman/listinfo/rtk-users > > > > > > >
_______________________________________________ Rtk-users mailing list [email protected] https://public.kitware.com/mailman/listinfo/rtk-users
