[prev in list] [next in list] [prev in thread] [next in thread]
List: insight-users
Subject: Re: [ITK-users] RT Structure Files Have Negative Indexes
From: <Jason.Dowling () csiro ! au>
Date: 2015-12-15 1:06:31
Message-ID: 55F4C48F3D67D84ABD1C7A670EC51C801B63C883 () exmbx03-cdc ! nexus ! csiro ! au
[Download RAW message or body]
Hi Jared,
That's a bit strange. If you are able, feel free to send me the DICOM-RT f=
iles 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?
All the best,
Jason
From: Andras Lasso [mailto:lasso@queensu.ca]
Sent: Tuesday, 15 December 2015 2:59 AM
To: Becksfort, Jared <Jared.Becksfort@STJUDE.ORG>; insight-users@itk.org; D=
owling, Jason (H&B, Herston - RBWH) <Jason.Dowling@csiro.au>
Subject: RE: RT Structure Files Have Negative Indexes
You might also use 3D Slicer with SlicerRT extension (www.slicerrt.org<http=
://www.slicerrt.org>) 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.
Andras
From: Community [mailto:community-bounces@itk.org] On Behalf Of Becksfort, =
Jared
Sent: Monday, December 14, 2015 1:49 AM
To: insight-users@itk.org<mailto:insight-users@itk.org>; Jason.Dowling@csir=
o.au<mailto:Jason.Dowling@csiro.au>
Subject: [ITK] [ITK-users] RT Structure Files Have Negative Indexes
Hello,
I am trying to extract RT structure files into Niftii maps using the progra=
m found at http://www.insight-journal.org/browse/publication/887.
I have compiled it, and it runs successfully with the test data, yielding c=
orrect 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:
Inserting region with 551 points into slice: -122
It also complains about contour points being outside the boundary, probably=
due to the negative indexes.
I am attaching the output. I am not completely sure I can attach the RT fi=
le yet, as it is actual patient data. I can find out and do so if that hel=
ps. 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?
Thanks,
Jared
[Attachment #3 (text/html)]
<html xmlns:v="urn:schemas-microsoft-com:vml" \
xmlns:o="urn:schemas-microsoft-com:office:office" \
xmlns:w="urn:schemas-microsoft-com:office:word" \
xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" \
xmlns="http://www.w3.org/TR/REC-html40"> <head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
p.p1, li.p1, div.p1
{mso-style-name:p1;
mso-style-priority:99;
margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
span.EmailStyle19
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:#1F497D;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-AU" link="blue" vlink="purple">
<div class="WordSection1">
<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>
<div>
<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>
<p class="MsoNormal"><span lang="EN-GB" \
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
</div>
<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>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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> </div>
</div>
<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>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<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> </div>
</div>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<div id="divtagdefaultwrapper">
<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>
</div>
</div>
</body>
</html>
_____________________________________
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Kitware offers ITK Training Courses, for more information visit:
http://www.kitware.com/products/protraining.php
Please keep messages on-topic and check the ITK FAQ at:
http://www.itk.org/Wiki/ITK_FAQ
Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/insight-users
--===============1869093212==--
[prev in list] [next in list] [prev in thread] [next in thread]
Configure |
About |
News |
Add a list |
Sponsored by KoreLogic