Hi James, Good that it works. I know it is a work-around and not a real solution. I'll look into how to best do the check. (And then create a pull request on GitHub)
Best regards Andreas On Wed, 8 Aug 2018, 12:49 Korte James, <[email protected]> wrote: > Hi Andreas, > > > > Everything works now! Can’t believe I missed this… should have kept > scrolling till the final projection. > > > > Perhaps a check could be added to the code, the .xml file has a count > field that could be matched to the number of projection files selected by > the regex? > > > > Thanks for your help! > > > > Cheers, > > James > > > > > > *From:* Andreas Andersen [mailto:[email protected]] > *Sent:* Wednesday, 8 August 2018 5:21 PM > *To:* Korte James > *Cc:* [email protected] > *Subject:* Re: [Rtk-users] Reconstructing from TrueBeam data > > > > Hi James, > > The probeam and truebeam .xim format should be the same. > > Sometimes the last projection is empty, which could cause problems like > what you see. > > Moving, deleting, or just renaming, the last projection should solve that > problem. > > Let me know if this works for you. > > > > Best regards > > Andreas > > > > > > On Wed, 8 Aug 2018, 07:31 Korte James, <[email protected]> wrote: > > Hi, > > > > I’m having some issues reconstructing CBCT data from a Varian TrueBeam > system. > > > > Just wondering if I am doing something really stupid? Does RTK support > imaging data off a TrueBeam system? > > > > I found a good masters thesis where they modified RTK and pre-processed > TrueBeam data, but wanted to get some feedback before investing time into a > custom solution ( > https://open.library.ubc.ca/cIRcle/collections/ubctheses/24/items/1.0167188 > ) > > > > I’ve just been using the RTK command line interface. First creating a > geometry file using “rtkvarianprobeamgeometry.exe” as the Scan.xml file > from our TrueBeam data has a very similar structure to the Scan.xml from > the RTK probeam example: > > rtkvarianprobeamgeometry.exe -v -x Scan.xml -o geometry.xml -p > Acquisitions\763250797\ -r Proj.*.xim > > > > I then try to reconstruct using the FDK algorithm using the following > command: > > rtkfdk.exe -v -g geometry.xml -o slices.mha -p Acquisitions\763250797\ -r > Proj.*.xim > > > > And I get the following error: > > Regular expression matches 893 file(s)... > > Reading... > > ExceptionObject caught with reader->Update() in file c:\path-to-rtk-src\rtk > > \applications\rtkfdk\rtkfdk.cxx line 63 > > > > itk::InvalidRequestedRegionError (00000000002FDFF8) > > Location: "void __cdecl itk::ImageFileReader<class itk::Image<unsigned > int,3>,cl > > ass itk::DefaultConvertPixelTraits<unsigned int> > >::EnlargeOutputRequestedRegion > > (class itk::DataObject *)" > > File: > c:\path-to-itk-src\src\modules\io\imagebase\include\itkimagefilereader.hxx > > Line: 350 > > Description: ImageIO returns IO region that does not fully contain the > requested > > regionRequested region: ImageRegion (00000000002FDC48) > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [1024, 768, 1] > > StreamableRegion region: ImageRegion (00000000002FDBF8) > > Dimension: 3 > > Index: [0, 0, 0] > > Size: [0, 0, 1] > > > > > > Cheers! > > James Korte > > > > *Disclaimer:* This email (including any attachments or links) may contain > confidential and/or legally privileged information and is intended only to > be read or used by the addressee. If you are not the intended addressee, > any use, distribution, disclosure or copying of this email is strictly > prohibited. Confidentiality and legal privilege attached to this email > (including any attachments) are not waived or lost by reason of its > mistaken delivery to you. If you have received this email in error, please > delete it and notify us immediately by telephone or email. Peter MacCallum > Cancer Centre provides no guarantee that this transmission is free of virus > or that it has not been intercepted or altered and will not be liable for > any delay in its receipt. > > _______________________________________________ > Rtk-users mailing list > [email protected] > https://public.kitware.com/mailman/listinfo/rtk-users > > *Disclaimer:* This email (including any attachments or links) may contain > confidential and/or legally privileged information and is intended only to > be read or used by the addressee. If you are not the intended addressee, > any use, distribution, disclosure or copying of this email is strictly > prohibited. Confidentiality and legal privilege attached to this email > (including any attachments) are not waived or lost by reason of its > mistaken delivery to you. If you have received this email in error, please > delete it and notify us immediately by telephone or email. Peter MacCallum > Cancer Centre provides no guarantee that this transmission is free of virus > or that it has not been intercepted or altered and will not be liable for > any delay in its receipt. >
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