[Rtk-users] 4D Phase-correlated Reconstruction

Fri May 15 05:23:03 EDT 2020

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 <zhehao.zhang at wustl.edu>
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 <simon.rit at creatis.insa-lyon.fr>
> *Sent: *Thursday, May 14, 2020 2:17 AM
> *To: *Zhang, Zhehao <zhehao.zhang at wustl.edu>
> *Cc: *rtk-users at public.kitware.com
> *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 <zhehao.zhang at wustl.edu>
> 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 <simon.rit at creatis.insa-lyon.fr>
> *Sent: *Wednesday, May 13, 2020 3:59 AM
> *To: *Zhang, Zhehao <zhehao.zhang at wustl.edu>
> *Cc: *rtk-users at public.kitware.com
> *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 <zhehao.zhang at wustl.edu>
> 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
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
>
>
>
>
> *From: *Zhang, Zhehao <zhehao.zhang at wustl.edu>
> *Sent: *Thursday, May 14, 2020 2:38 AM
> *To: *Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Cc: *rtk-users at public.kitware.com
> *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 <simon.rit at creatis.insa-lyon.fr>
> *Sent: *Thursday, May 14, 2020 2:17 AM
> *To: *Zhang, Zhehao <zhehao.zhang at wustl.edu>
> *Cc: *rtk-users at public.kitware.com
> *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 <zhehao.zhang at wustl.edu>
> 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 <simon.rit at creatis.insa-lyon.fr>
> *Sent: *Wednesday, May 13, 2020 3:59 AM
> *To: *Zhang, Zhehao <zhehao.zhang at wustl.edu>
> *Cc: *rtk-users at public.kitware.com
> *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 <zhehao.zhang at wustl.edu>
> 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
> Rtk-users at public.kitware.com
> https://public.kitware.com/mailman/listinfo/rtk-users
>
>
>
>
>
>
>
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