[vtkusers] Exploded view

Fri Oct 31 20:57:38 EDT 2014

Hey there,

I’ll try to go through you description:

> I have just started a PhD looking at a brain cancers. I am currently hoping
> to create an applet that will display the areas of interest around the
> cancer.

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

> Just after surgery, the cancerous area is empty, so I was contemplating the
> idea of doing edge detection of a CT DICOM to find where the air meets
> tissue to visualise where the tumour was.

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: http://pyscience.wordpress.com/2014/09/11/surface-extraction-creating-a-mesh-from-pixel-data-using-python-and-vtk/ <http://pyscience.wordpress.com/2014/09/11/surface-extraction-creating-a-mesh-from-pixel-data-using-python-and-vtk/>). 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: http://pyscience.wordpress.com/2014/10/19/image-segmentation-with-python-and-simpleitk/ <http://pyscience.wordpress.com/2014/10/19/image-segmentation-with-python-and-simpleitk/>). SimpleITK also allows you to load compressed DICOM data through GDCM which AFAIK VTK doesn’t.

> After I have found the volume, it should be simple enough to calculate the
> centre of mass of the tumour. Following this, I think I would like to create
> 3 orthogonal cutting planes going through the brain so that the brain is
> split into 8 parts, centered around the tumour.

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: https://gist.github.com/somada141/3d426b181ce202933950 <https://gist.github.com/somada141/3d426b181ce202933950>).

If you actually want to visualize the extracted surfaces as split you can clip them

> Is this feasible?

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.

Anyway, good luck with the PhD, sound interesting :)

Cheers,
Adam

> On Nov 1, 2014, at 2:49 AM, mbcx9rb9 <richard.j.brown at live.co.uk> wrote:
> 
> I have just started a PhD looking at a brain cancers. I am currently hoping
> to create an applet that will display the areas of interest around the
> cancer.
> 
> Just after surgery, the cancerous area is empty, so I was contemplating the
> idea of doing edge detection of a CT DICOM to find where the air meets
> tissue to visualise where the tumour was.
> 
> After I have found the volume, it should be simple enough to calculate the
> centre of mass of the tumour. Following this, I think I would like to create
> 3 orthogonal cutting planes going through the brain so that the brain is
> split into 8 parts, centered around the tumour.
> 
> I would hope to show this all as an exploded view so that I can display the
> tumor, and the 8 other segments all side by side. I want to do this so that
> I can run GATE simulations on the uptake of activity in the tumourous area
> and the healthy sections touching it and see the results as a function of
> colour.
> 
> Is this feasible?
> 
> If I haven't explained how I envisage the final visualisation, imagine a
> peach - take out the stone and cut the rest into 8ths (half it, half those,
> and half all those). I want to show the stone and the 8ths with specific
> focus on the areas of the peach that were touching the stone.
> 
> Thanks in advance for the help
> 
> 
> 
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