<p dir="ltr">The TubeTK extension is currently not enabled, but will be again shortly (and it should build now). However maybe someone on that list will be able to better advise which algorithm specifically you would want for centerline extraction.</p>
<div class="gmail_quote">On Dec 2, 2013 8:02 PM, "Andras Lasso" <<a href="mailto:lasso@queensu.ca">lasso@queensu.ca</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">I think the trickiest part is that you need to determine the vessel centerline. Once you have that, the cross-section measurement is straightforward (can be
implemented in 20-30 lines of Python code).<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">The VMTK and TubeTK extensions should be able to do centerline extraction, but I don’t know the current status of these extensions. Some developers of these
toolkits are on the mailing list, so hopefully they will chime in.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Andras<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><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""> <a href="mailto:slicer-users-bounces@bwh.harvard.edu" target="_blank">slicer-users-bounces@bwh.harvard.edu</a> [mailto:<a href="mailto:slicer-users-bounces@bwh.harvard.edu" target="_blank">slicer-users-bounces@bwh.harvard.edu</a>]
<b>On Behalf Of </b>Andrew Bond<br>
<b>Sent:</b> November 29, 2013 9:49 AM<br>
<b>To:</b> <a href="mailto:slicer-users@bwh.harvard.edu" target="_blank">slicer-users@bwh.harvard.edu</a><br>
<b>Subject:</b> [slicer-users] Calculating cross-sectional area from 3D volume<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Hi,<u></u><u></u></p>
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<p class="MsoNormal">I am looking at disease in blood vessels. So far, I have managed to segment out and measure the volumes of various components in the whole vessel. If possible, I would now like to calculate the cross-sectional areas of the same segmented
components at various points throughout the vessel e.g. at 100micrometer intervals, so we can draw comparisons to histological sectioning. As a last resort I could look at individual slices and measure manually, but was hoping there would be a more automated
way. <u></u><u></u></p>
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<p class="MsoNormal">Is there a module to enable me to do this? I am currently using Slicer version <span style="font-size:11.0pt">4.2.2-1 r21513.</span> <u></u><u></u></p>
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<p class="MsoNormal">Any help would be gratefully received.<u></u><u></u></p>
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<p class="MsoNormal">Cheers,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Andy <u></u><u></u></p>
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<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
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