<div dir="auto">Hi James, <div dir="auto"><br></div><div dir="auto">Good that it works. </div><div dir="auto">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) </div><div dir="auto"><br></div><div dir="auto">Best regards </div><div dir="auto">Andreas</div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, 8 Aug 2018, 12:49 Korte James, <<a href="mailto:James.Korte@petermac.org">James.Korte@petermac.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-AU" link="blue" vlink="purple">
<div class="m_-7927859316796087648WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Hi Andreas,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Everything works now! Can’t believe I missed this… should have kept scrolling till the final projection.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">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?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Thanks for your help!
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Cheers,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">James</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif"">
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Andreas Andersen [mailto:<a href="mailto:andreasga22@gmail.com" target="_blank" rel="noreferrer">andreasga22@gmail.com</a>]
<br>
<b>Sent:</b> Wednesday, 8 August 2018 5:21 PM<br>
<b>To:</b> Korte James<br>
<b>Cc:</b> <a href="mailto:rtk-users@public.kitware.com" target="_blank" rel="noreferrer">rtk-users@public.kitware.com</a><br>
<b>Subject:</b> Re: [Rtk-users] Reconstructing from TrueBeam data<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">Hi James, <u></u><u></u></p>
<div>
<p class="MsoNormal">The probeam and truebeam .xim format should be the same. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> Sometimes the last projection is empty, which could cause problems like what you see.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Moving, deleting, or just renaming, the last projection should solve that problem. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Let me know if this works for you. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Best regards<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Andreas<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">On Wed, 8 Aug 2018, 07:31 Korte James, <<a href="mailto:James.Korte@petermac.org" target="_blank" rel="noreferrer">James.Korte@petermac.org</a>> wrote:<u></u><u></u></p>
</div>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<div>
<div>
<p class="MsoNormal">Hi,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">I’m having some issues reconstructing CBCT data from a Varian TrueBeam system.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Just wondering if I am doing something really stupid? Does RTK support imaging data off a TrueBeam system?<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">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 (<a href="https://open.library.ubc.ca/cIRcle/collections/ubctheses/24/items/1.0167188" target="_blank" rel="noreferrer">https://open.library.ubc.ca/cIRcle/collections/ubctheses/24/items/1.0167188</a>)<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">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:<u></u><u></u></p>
<p class="MsoNormal">rtkvarianprobeamgeometry.exe -v -x Scan.xml -o geometry.xml -p Acquisitions\763250797\ -r Proj.*.xim<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">I then try to reconstruct using the FDK algorithm using the following command:<u></u><u></u></p>
<p class="MsoNormal">rtkfdk.exe -v -g geometry.xml -o slices.mha -p Acquisitions\763250797\ -r Proj.*.xim<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">And I get the following error:<u></u><u></u></p>
<p class="MsoNormal">Regular expression matches 893 file(s)...<u></u><u></u></p>
<p class="MsoNormal">Reading...<u></u><u></u></p>
<p class="MsoNormal">ExceptionObject caught with reader->Update() in file c:\path-to-rtk-src\rtk<u></u><u></u></p>
<p class="MsoNormal">\applications\rtkfdk\rtkfdk.cxx line 63<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">itk::InvalidRequestedRegionError (00000000002FDFF8)<u></u><u></u></p>
<p class="MsoNormal">Location: "void __cdecl itk::ImageFileReader<class itk::Image<unsigned int,3>,cl<u></u><u></u></p>
<p class="MsoNormal">ass itk::DefaultConvertPixelTraits<unsigned int> >::EnlargeOutputRequestedRegion<u></u><u></u></p>
<p class="MsoNormal">(class itk::DataObject *)"<u></u><u></u></p>
<p class="MsoNormal">File: c:\path-to-itk-src\src\modules\io\imagebase\include\itkimagefilereader.hxx<u></u><u></u></p>
<p class="MsoNormal">Line: 350<u></u><u></u></p>
<p class="MsoNormal">Description: ImageIO returns IO region that does not fully contain the requested<u></u><u></u></p>
<p class="MsoNormal">regionRequested region: ImageRegion (00000000002FDC48)<u></u><u></u></p>
<p class="MsoNormal"> Dimension: 3<u></u><u></u></p>
<p class="MsoNormal"> Index: [0, 0, 0]<u></u><u></u></p>
<p class="MsoNormal"> Size: [1024, 768, 1]<u></u><u></u></p>
<p class="MsoNormal">StreamableRegion region: ImageRegion (00000000002FDBF8)<u></u><u></u></p>
<p class="MsoNormal"> Dimension: 3<u></u><u></u></p>
<p class="MsoNormal"> Index: [0, 0, 0]<u></u><u></u></p>
<p class="MsoNormal"> Size: [0, 0, 1]<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Cheers!<u></u><u></u></p>
<p class="MsoNormal">James Korte<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<p><strong><span style="font-size:8.5pt">Disclaimer:</span></strong><span style="font-size:8.5pt"> 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.<u></u><u></u></span></p>
</div>
<p class="MsoNormal">_______________________________________________<br>
Rtk-users mailing list<br>
<a href="mailto:Rtk-users@public.kitware.com" target="_blank" rel="noreferrer">Rtk-users@public.kitware.com</a><br>
<a href="https://public.kitware.com/mailman/listinfo/rtk-users" target="_blank" rel="noreferrer">https://public.kitware.com/mailman/listinfo/rtk-users</a><u></u><u></u></p>
</blockquote>
</div>
</div>
</div>
<p style="FONT-SIZE:11px"><font><strong>Disclaimer:</strong> 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.</font></p></div>
</blockquote></div>