[Rtk-users] Reconstructing from TrueBeam data

[Andreas Andersen]

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, <James.Korte at petermac.org> 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:andreasga22 at gmail.com]
> *Sent:* Wednesday, 8 August 2018 5:21 PM
> *To:* Korte James
> *Cc:* rtk-users at public.kitware.com
> *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, <James.Korte at petermac.org> 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
>
>
>
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