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<p class="MsoNormal"><span 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 style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Andras<o:p></o:p></span></p>
<p class="MsoNormal"><span 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 style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Community [mailto:community-bounces@itk.org]
<b>On Behalf Of </b>Becksfort, Jared<br>
<b>Sent:</b> Monday, December 14, 2015 1:49 AM<br>
<b>To:</b> insight-users@itk.org; Jason.Dowling@csiro.au<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"><o:p> </o:p></p>
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<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Hello,<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span 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 style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span 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 style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="p1" style="background:white"><span 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 style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span 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 style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span 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 style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Thanks,<o:p></o:p></span></p>
<p style="background:white"><span style="font-family:"Calibri",sans-serif;color:black">Jared<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
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