[Insight-users] I need help on tuning Laplacian Level Set Segmentation (LaplacianSegmentationLevelSetImageFilter.cxx)

[John Drozd]

Hello,
I have performed a reasonable fuzzy connectedness segmentation (that I
modified to use multiple seeds) of lateral human brain ventricles in an MRI
brain image of a mildly cognitive impaired person that I obtained from the
ADNI database.
Prior to performing the fuzzy connectedness segmentation, I smoothed the
noise and enhanced the edges using an Anisotropic Diffusion filter.
I am trying to use this fuzzy connectedness segmentation as my initial level
set for a level set segmentation but when performing a Laplacian Level
Set segmentation, I get a pitted volume.
I think the following are my problems.
1) When I load the label map from the fuzzy connectedness segmentation into
3D Slicer to view it, I get Fg: None and Bg: 1 for the segmented volume, and
Fg: None and Bg: 0 for the black area that surrounds the ventricles.  I
think that I am setting my foreground and background values incorrectly. I
feel this is a problem because I need to specify an isovalue midway between
the foreground and background values.  I can send you my fuzzy connectedness
and Laplacian level set segmentation code if this would help you be able to
help me.  Also, the laplacian level set segmentation performs anisotropic
diffusion. Because I perform this prior to my fuzzy connectedness
segmentation, I am essentially performing anisotropic diffusion twice.
Could this be a problem?
2) Also, how do you run the level set segmentation to go to convergence. Do
you just input a large maximum number of iterations?
3) Also how can I use the outputted "speedImage.mha" figure to help me tune
my parameters for "DiffusionIterations", "DiffusionConductance",
"PropagationWeight", "InitialModelIsovalue" and "MaximumIterations".  I can
send you the speed image as well.
4) Also, the level set segmentation only performs 1 iteration eventhough I
specified a maximum 100 iterations.  Should I use a smaller RMS error than
0.002?

Any help would be appreciated.

Thanks for your time,

John

-- 
John Drozd
Post-Doctoral Fellow, Robarts Research Institute
The University of Western Ontario
London, ON, Canada
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