<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hey there,<div class=""><br class=""></div><div class="">I’ll try to go through you description:</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">I have just started a PhD looking at a brain cancers. I am currently hoping<br class="">to create an applet that will display the areas of interest around the<br class="">cancer.</blockquote><br class=""></div><div class="">Not sure how you envision said applet but if you’re referring to a web-applet then you could take a look at VTK Web or ParaviewWeb which you allow in-browser visualization of your scene</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">Just after surgery, the cancerous area is empty, so I was contemplating the<br class="">idea of doing edge detection of a CT DICOM to find where the air meets<br class="">tissue to visualise where the tumour was.</blockquote><br class=""></div><div class="">You could easily do some basic segmentation based on the CT Hounsfield units using thresholding in VTK and create labelfields and 3D surfaces (check this blog post on surface extraction: <a href="http://pyscience.wordpress.com/2014/09/11/surface-extraction-creating-a-mesh-from-pixel-data-using-python-and-vtk/" class="">http://pyscience.wordpress.com/2014/09/11/surface-extraction-creating-a-mesh-from-pixel-data-using-python-and-vtk/</a>). I can’t vouch for the availability or ease-of-use of advanced segmentation algorithms in VTK but ITK/SimpleITK has all that functionality (check this other blog post on SimpleITK and image segmentation: <a href="http://pyscience.wordpress.com/2014/10/19/image-segmentation-with-python-and-simpleitk/" class="">http://pyscience.wordpress.com/2014/10/19/image-segmentation-with-python-and-simpleitk/</a>). SimpleITK also allows you to load compressed DICOM data through GDCM which AFAIK VTK doesn’t.</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">After I have found the volume, it should be simple enough to calculate the<br class="">centre of mass of the tumour. Following this, I think I would like to create<br class="">3 orthogonal cutting planes going through the brain so that the brain is<br class="">split into 8 parts, centered around the tumour.</blockquote><br class=""></div><div class="">That’s actually easy in VTK. After you’ve extracted the tumor surface as vtkPolyData (again, surface extraction) you can use vtkCenterOfMass to find that point. Then you just need 3 cross-sections through the vtkImageData (containing the DICOM data) through the vtkImageSliceMapper (check this gist — haven’t written a blog post on that yet: <a href="https://gist.github.com/somada141/3d426b181ce202933950" class="">https://gist.github.com/somada141/3d426b181ce202933950</a>).</div><div class=""><br class=""></div><div class="">If you actually want to visualize the extracted surfaces as split you can clip them</div><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">Is this feasible?</blockquote><br class=""></div><div class="">AFAI understand by your description I’d say a combination of VTK and ITK/SimpleITK gives you all the tools you need so I dare say it is feasible if not completely straightforward. You probably know better, but I was under the impression that after extravasation the tumor-hole is filled with cotton to soak up fluid so I’m not 100% sure you will get a clearly demarcated air-hole there. Segmentation might be a lil’ more tricky then.</div><div class=""><br class=""></div><div class="">Anyway, good luck with the PhD, sound interesting :)</div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">Adam</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 1, 2014, at 2:49 AM, mbcx9rb9 <<a href="mailto:richard.j.brown@live.co.uk" class="">richard.j.brown@live.co.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">I have just started a PhD looking at a brain cancers. I am currently hoping<br class="">to create an applet that will display the areas of interest around the<br class="">cancer.<br class=""><br class="">Just after surgery, the cancerous area is empty, so I was contemplating the<br class="">idea of doing edge detection of a CT DICOM to find where the air meets<br class="">tissue to visualise where the tumour was.<br class=""><br class="">After I have found the volume, it should be simple enough to calculate the<br class="">centre of mass of the tumour. Following this, I think I would like to create<br class="">3 orthogonal cutting planes going through the brain so that the brain is<br class="">split into 8 parts, centered around the tumour.<br class=""><br class="">I would hope to show this all as an exploded view so that I can display the<br class="">tumor, and the 8 other segments all side by side. I want to do this so that<br class="">I can run GATE simulations on the uptake of activity in the tumourous area<br class="">and the healthy sections touching it and see the results as a function of<br class="">colour.<br class=""><br class="">Is this feasible?<br class=""><br class="">If I haven't explained how I envisage the final visualisation, imagine a<br class="">peach - take out the stone and cut the rest into 8ths (half it, half those,<br class="">and half all those). I want to show the stone and the 8ths with specific<br class="">focus on the areas of the peach that were touching the stone.<br class=""><br class="">Thanks in advance for the help<br class=""><br class=""><br class=""><br class="">--<br class="">View this message in context: <a href="http://vtk.1045678.n5.nabble.com/Exploded-view-tp5729301.html" class="">http://vtk.1045678.n5.nabble.com/Exploded-view-tp5729301.html</a><br class="">Sent from the VTK - Users mailing list archive at <a href="http://Nabble.com" class="">Nabble.com</a>.<br class="">_______________________________________________<br class="">Powered by <a href="http://www.kitware.com" class="">www.kitware.com</a><br class=""><br class="">Visit other Kitware open-source projects at <a href="http://www.kitware.com/opensource/opensource.html" class="">http://www.kitware.com/opensource/opensource.html</a><br class=""><br class="">Please keep messages on-topic and check the VTK FAQ at: <a href="http://www.vtk.org/Wiki/VTK_FAQ" class="">http://www.vtk.org/Wiki/VTK_FAQ</a><br class=""><br class="">Follow this link to subscribe/unsubscribe:<br class=""><a href="http://public.kitware.com/mailman/listinfo/vtkusers" class="">http://public.kitware.com/mailman/listinfo/vtkusers</a><br class=""></div></blockquote></div><br class=""></div></body></html>