Dear Andreas, Today we had the RTK training and some users were looking for a XIM file reader. I pointed to your contributions but any chance to have it put in RTK soon? Thanks in advance, Simon
On Mon, Sep 19, 2016 at 9:26 AM, Simon Rit <[email protected]> wrote: > Hi, > Thanks for sharing. There still seems to be some streak artefacts, do you > see the same in the Varian reconstruction? > I'm looking forward to the pull-request, I think we should try to make the > bzip2 optional. > Simon > > On Fri, Sep 16, 2016 at 10:37 PM, Andreas Gravgaard Andersen < > [email protected]> wrote: > >> Thanks for the fast response Simon! >> >> I flipped the angles (360 - angle[deg]) and it worked! Thanks, you were >> right all along! >> I just didn't get why it makes a difference. I think I do now, as the >> resulting image was flipped upside down and not left/right as I expected. >> [attached] >> >> The reconstruction is significantly better, I'll look into what should be >> included in the reader and what I should keep in my program to keep >> conformity with the other readers. Then I'll create a pull request. >> >> Just for the purpose of others hitting the same or a similar bug, I also >> attempted: >> I did the SART reconstruction with 10 iterations, lambda=0.3, and Joseph >> back/forward projection, *but with no* significant improvement [attached] >> >> And: >> If you want you can download the data set from: [Dropbox link to 460MB >> zip <https://www.dropbox.com/s/hg2k50vw3f7bt4b/CatPhan.zip?dl=0> (I'll >> keep it up as long as Dropbox allows me)] Only the Acquisitions/subfolder >> is used along with the Scan.xml (Calibrations folder may be used in the >> future in my program, but I'm not sure if you can rely on the existence of >> the content). >> >> A MatLab XimReader is available: link >> <https://github.com/agravgaard/RTK/blob/master/code/ReadXim.m> (also >> available from Varian bitbucket along a with a python version and a >> C#->matlab plugin >> <https://bitbucket.org/dmoderesearchtools/ximreader/downloads>). >> Otherwise my fork with the RTK-style reader is available from the same >> repository (I have also added Hnc support, thanks to the Geoff Hugo fork, >> so bzip2 is a new dependancy). >> >> Best regards >> Andreas >> >> >> __________________________________ >> >> Andreas Gravgaard Andersen >> >> Department of Oncology, >> >> Aarhus University Hospital >> >> Nørrebrogade 44, >> >> 8000, Aarhus C >> >> Mail: [email protected] >> >> Cell: +45 3165 8140 >> >> >> >> 2016-09-16 16:13 GMT+02:00 Simon Rit <[email protected]>: >> >>> Hi, >>> You can try any iterative reconstruction, they can also handle short >>> scans. Start with a few iterations of rtksart or rtkconjugategradient. >>> However, the nature of the artifacts indicate more a problem in the >>> geometry in my opinion. I have seen such errors when, for example, rotating >>> in the wrong direction. I can have a look if you share the dataset. >>> Cheers, >>> Simon >>> >>> On Fri, Sep 16, 2016 at 2:56 PM, Andreas Gravgaard Andersen < >>> [email protected]> wrote: >>> >>>> Thanks for the suggestions, Simon and Cyril! >>>> >>>> I have been carefully looking though the geometry and from what I >>>> understand of the transformations matrices, the geometry looks correct/(as >>>> expected). >>>> >>>> HOWEVER: I found out that the reason for the Hnd to behave differently >>>> were because had used half-fan scans (full-arc). >>>> When I used a full-fan (half-arc) scan of Hnd projections the same >>>> artifacts occurs! >>>> >>>> Are there other (built-in) means of improving half-arc scans, than the >>>> parker short scan filter? >>>> >>>> Parker short scan does a decent job, but the result is still far from >>>> the quality of the Varian software reconstruction at least for the CatPhan. >>>> >>>> Best regards >>>> Andreas >>>> >>>> >>>> __________________________________ >>>> >>>> Andreas Gravgaard Andersen >>>> >>>> Department of Oncology, >>>> >>>> Aarhus University Hospital >>>> >>>> Nørrebrogade 44, >>>> >>>> 8000, Aarhus C >>>> >>>> Mail: [email protected] >>>> >>>> Cell: +45 3165 8140 >>>> >>>> >>>> >>>> 2016-09-14 9:10 GMT+02:00 Cyril Mory <[email protected]>: >>>> >>>>> One suggestion since it works with the Hnd projections: >>>>> You can run rtkprojections twice (with the Hnd projections, then with >>>>> Xim projections) and output two projection stack files and two geometry >>>>> files, then compare the projection stack files by subtracting one to the >>>>> other (with SimpleRTK or clitk) and the geometry files with diff. If they >>>>> are identical, then I do not see any reason why the reconstructions should >>>>> be different, so my guess is that you will find differences. >>>>> >>>>> >>>>> On 09/13/2016 10:18 PM, Simon Rit wrote: >>>>> >>>>>> Hi, >>>>>> I have almost never worked with Varian data but it looks like a >>>>>> geometry problem. Maybe the problem comes from a bad ordering of the >>>>>> projections which results in assigning a bad geometry to each >>>>>> projection. How did you name your projections? Maybe check that the >>>>>> order matches that of the RTK geometry file. Otherwise, there might be >>>>>> an issue in the creation of the geometry file itself. >>>>>> All this sounds good, happy bug hunt and don't hesitate to share your >>>>>> code when you feel it's ready. >>>>>> Simon >>>>>> >>>>>> On Tue, Sep 13, 2016 at 7:06 PM, Andreas Gravgaard Andersen >>>>>> <[email protected]> wrote: >>>>>> >>>>>>> Dear RTK experts, >>>>>>> >>>>>>> I am reconstructing Varian ProBeam projections of the Xim image >>>>>>> format. I >>>>>>> have written the reader myself - very similar to the Hnd one already >>>>>>> available with RTK. >>>>>>> Links to my fork: [XimReader, XMLReader, GeometryReader] >>>>>>> >>>>>>> The reader apparently works (Images and angles displays as expected >>>>>>> in UI), >>>>>>> however when reconstructing with a regular FDK I get a reconstructed >>>>>>> image >>>>>>> that is smeared out around the high and low density areas [see >>>>>>> attached >>>>>>> image] >>>>>>> >>>>>>> I'm using half arc, full fan images with no bow-tie filter from >>>>>>> Scripps >>>>>>> (~520 projections). Fixed detector and source (offset=0) with SID=2m, >>>>>>> SDD=3m. >>>>>>> >>>>>>> For the Hnd projections the reconstruction works perfectly (Same >>>>>>> algorithm). >>>>>>> The reconstruction of the Xim projections performed on Varian >>>>>>> software works >>>>>>> perfectly. >>>>>>> >>>>>>> Without the Parker Short Scan Filter the first and last projections >>>>>>> creates >>>>>>> streaks across the reconstruction as if they were way too bright. >>>>>>> If the first few projections are excluded, the following projection >>>>>>> will act >>>>>>> the same way. >>>>>>> >>>>>>> The projections are corrected for beam hardening and all the >>>>>>> projections >>>>>>> have the expected attenuation. >>>>>>> No "smearing" filters (like median) is used, and iterative >>>>>>> reconstruction >>>>>>> makes the same artifacts. >>>>>>> >>>>>>> Setting the value of the first and last projection to zero has the >>>>>>> same >>>>>>> effect as excluding. Changing the ramp filter only changes noise, >>>>>>> not the >>>>>>> artifacts. >>>>>>> >>>>>>> Have any of you had a similar problem? Am I missing something? >>>>>>> Any suggestions are welcome I'm running out of ideas. >>>>>>> >>>>>>> Best regards >>>>>>> Andreas >>>>>>> >>>>>>> __________________________________ >>>>>>> >>>>>>> Andreas Gravgaard Andersen >>>>>>> >>>>>>> Department of Oncology, >>>>>>> >>>>>>> Aarhus University Hospital >>>>>>> >>>>>>> Nørrebrogade 44, >>>>>>> >>>>>>> 8000, Aarhus C >>>>>>> >>>>>>> Mail: [email protected] >>>>>>> >>>>>>> Cell: +45 3165 8140 >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Rtk-users mailing list >>>>>>> [email protected] >>>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>>> >>>>>>> _______________________________________________ >>>>>> Rtk-users mailing list >>>>>> [email protected] >>>>>> http://public.kitware.com/mailman/listinfo/rtk-users >>>>>> >>>>>> >>>>> >>>> >>> >> >
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