[Insight-users] Re: [Paraview] Binary Thresholding and Isosurface Generation

[Luis Ibanez]

Hi Kevin,

The way ParaView (and VTK for that matter) generates contours
is not by selecting black regions, but by specifying a value
for an iso-surface in the image.

If you have already a segmentation of the bony structures,
you can generate surfaces for the bony structures themselves.

As far as the spinal cord goes, you probably want to get first
a segmentation of it, and then use ParaView (or a VTK pipeline)
in order to visualize the result.  ITK segmentation methods
that you may want to try are:

   - Region Growing
   - Tubes Level Set
   - Watershed

You will find description of all these methods in the
ITK Software Guide


    http://www.itk.org/ItkSoftwareGuide.pdf


If you still have questions, it would be useful if you could
post your dataset so we can take a look at it.



   Regards,


      Luis



----------------------
Kevin Ming wrote:
> Hi Luis,
> 
> I have a 3D MRI of a spinal column from which I want to be able to 
> visualize the spinal cord within the bony sections.  I've been able to 
> get the bony section quite well, but within it (where the spinal cord 
> resides), I have an empty column.  I thought that perhaps it's because 
> ParaView generates contours for black intenities of the image and leaves 
> all the white intenities empty.  So I inverted my 3D data using the 
> BinaryThresholdImageFilter, hopeing that ParaView would now be able to 
> generate just the spinal cord (now that it's black) and leave the bony 
> spinal column (now that it's white).  Unfortunately, I get pretty much 
> the same visualization as before I did the inversion.  What do you think 
> I should do?
> 
> 
> Thank you,
> Kevin
> 
> On 7/20/06, *Luis Ibanez* <luis.ibanez at kitware.com 
> <mailto:luis.ibanez at kitware.com>> wrote:
> 
> 
> 
>     Hi Kevin,
> 
> 
>     Since both of your images are binary, and one is the inverse
>     of the other, it is normal that the iso-contour generated by
>     ParaView is the same for both images.
> 
> 
>     This should be the case, regarldess what iso-contour extraction
>     method you use. But, just for the record, what ParaView uses is
>     the vtkContourFilter:
> 
> 
>           http://www.vtk.org/doc/release/5.0/html/a01263.html
>     <http://www.vtk.org/doc/release/5.0/html/a01263.html>
> 
> 
> 
>     What was your goal when you generated one image as the inverse
>     of the other ?
> 
> 
>     There may be a better way to achieve your goal....
> 
> 
>        Please let us konw,
> 
> 
>           Thanks
> 
> 
> 
>               Luis
> 
> 
> 
>     ------------------
>     Kevin Ming wrote:
>      > Hi,
>      >
>      > I have two 3D images, one being the intensity inverse of the other,
>      > produced using the BinaryThresholdImageFilter.  When I generated the
>      > isosurface rendering using ParaView, both renderings looked almost
>      > identical, given the same contour values.  I would expect one
>     rendering
>      > to display features the other one wouldn't be able to, and vice
>     versa,
>      > which is what I want.  How does ParaView generate isosurfaces?
>      >
>      >
>      > Thank you,
>      > Kevin
>      >
>      >
>      >
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