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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Jared,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">That’s a bit strange. If you are able, feel free to send me the DICOM-RT files privately to test (and also let me know which TPS these
contours were exported from?). If Slicer (or Plastimatch) extract the contours correctly could you also please let me know?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">All the best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Jason<o:p></o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#0099CC"><o:p> </o:p></span></b></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Andras Lasso [mailto:lasso@queensu.ca]
<br>
<b>Sent:</b> Tuesday, 15 December 2015 2:59 AM<br>
<b>To:</b> Becksfort, Jared <Jared.Becksfort@STJUDE.ORG>; insight-users@itk.org; Dowling, Jason (H&B, Herston - RBWH) <Jason.Dowling@csiro.au><br>
<b>Subject:</b> RE: RT Structure Files Have Negative Indexes<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">You might also use 3D Slicer with SlicerRT extension (<a href="http://www.slicerrt.org">www.slicerrt.org</a>) to import all kinds of RT data – including
structure sets – and save them as binary label maps or surfaces that are easy to load using ITK.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Andras<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Community [<a href="mailto:community-bounces@itk.org">mailto:community-bounces@itk.org</a>]
<b>On Behalf Of </b>Becksfort, Jared<br>
<b>Sent:</b> Monday, December 14, 2015 1:49 AM<br>
<b>To:</b> <a href="mailto:insight-users@itk.org">insight-users@itk.org</a>; <a href="mailto:Jason.Dowling@csiro.au">
Jason.Dowling@csiro.au</a><br>
<b>Subject:</b> [ITK] [ITK-users] RT Structure Files Have Negative Indexes<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">Hello,<o:p></o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">I am trying to extract RT structure files into Niftii maps using the program found at <a href="http://www.insight-journal.org/browse/publication/887" title="http://www.insight-journal.org/browse/publication/887
Cmd+Click or tap to follow the link" id="LPlnk513712">http://www.insight-journal.org/browse/publication/887</a>.<o:p></o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">I have compiled it, and it runs successfully with the test data, yielding correct masks. I then tried to run it on data given to me by a colleague. The output
shows there are some negative slice indexes such as:<o:p></o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="p1" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">Inserting region with 551 points into slice: -122<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">It also complains about contour points being outside the boundary, probably due to the negative indexes.<o:p></o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">I am attaching the output. I am not completely sure I can attach the RT file yet, as it is actual patient data. I can find out and do so if that helps. I
don't know anything about RT structure files yet. Does anyone have ideas of what I can tell my colleague who generated the files?<o:p></o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">Thanks,<o:p></o:p></span></p>
<p style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">Jared<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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