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

[John Drozd]

Hi again,

>
> I have made some progress on my own by randomly selecting an isovalue of
> 0.5.  Now my level set segmentation is no longer pitted, but it has the same
> volume in mm^3 as the initially inputted fuzzy connectedness segmentation.
> It only performed one iteration and the RMS change was 0.0014962.  The
> maximum RMS error was set to 0.002 and the maximum number of iterations was
> set to 100. The number of diffusion iterations was set to 10, the diffusion
> conductance was set to 2.0, the propagation weight was set to 1.0, the
> initial model isovalue was set to 0.5, and the maximum number of iterations
> was set to 100.
>
> Any further advice is welcome.
>
>
Thanks,
>


> John
>


> On Thu, Feb 3, 2011 at 12:11 PM, John Drozd <john.drozd at gmail.com> wrote:
>
>> 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
>>
>>
>
>
> --
> John Drozd
> Post-Doctoral Fellow, Robarts Research Institute
> The University of Western Ontario
> London, ON, Canada
>
>


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