Re: [vmtk-users] Level set segmentation references

[Luca A. <luc...@or...>]

Hi Evan,

On Mar 22, 2013, at 9:48 PM, Evan Kao wrote:

> Hello,
> 
> I am trying to segment a particular set of 3D-cine images with vmtklevelsetsegmentation, but the perhaps due to the shape of the vessel and/or quality of the images, the suggested settings of 300 0 0 1 isn't working well.  I've tried playing around with the level set deformation parameters, but the resultant shapes feel just as arbitrary as if I had simply used thresholds directly.  Can you recommend any guides or references that can explain in more depth (i.e. quantitatively) how the parameters affect the deformation, and/or also provide an explanation of the additional options available in vmtklevelsetsegmentation that weren't covered in the tutorials?

The level set parameters are those of itkGeodesicActiveContourLevelSetImageFilter and itkGeodesicActiveContourLevelSetFunction. 
http://www.itk.org/Doxygen/html/classitk_1_1GeodesicActiveContourLevelSetImageFilter.html
http://www.itk.org/Doxygen/html/classitk_1_1GeodesicActiveContourLevelSetFunction.html

The main reference for level set methods is
J. A. Sethian, "Level Set Methods and Fast Marching Methods", Cambridge University Press, 1996. 
but you can find a lot of material around.

You may want to take a look at my PhDThesis (good old times) at lantiga.github.com/about/

If you have noise issues, I suggest you to use a non-zero featurederivativesigma , which expresses the width of the 
gaussian kernel used for performing partial derivatives for the feature image. It's expressed in physical spatial units
(e.g. mm) and it's roughly related to the minimum scale that you'll end up detecting in the image - i.e. the noise below
that spatial scale is going to be filtered out, thus not affecting the evolution of level sets (again, roughly speaking).

Feel free to post a couple of screenshots of the problem you're having, so that replies can be more to the point.

Best,

Luca


> Thank you,
> Evan Kao
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