[Insight-users] Re: Segmentation of the left ventricle

[Luis Ibanez]

Hi Christian,


The general process that you are using for segmenting
the ventricle looks fine. I'm assuming that you are
after the region containing blood inside the left
ventricle, is that correct ?

- The Step of curvature anisotropic diffusion
   seems to be ok. You have to visually verify
   if the image looks fine after the smoothing.
   There are no rules about how much iterations
   of smoothing to apply. You simple look for
   a balance between reducing noise and avoiding
   to degrade the edges of the structure that
   you want to segment.

- The GradientMagnitudeRecursiveGaussian with
   sigma = 1, should be ok *IFF* your images have
   the spacing correctly defined in millimeters.

- The Alpha and Beta values for the sigmoid
   are probably the source of the problem.
   These values are critical in the preparation
   of the speed image to be passed to the
   LevelSet segmentation filter.

   Alpha = -0.5 and Beta = 1.0 are nominal default
   values. It is unlikely that they will work for
   your images.  Instructions on how to tune these
   values to your image are described in the
   SoftwareGuide

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

   The sigmoid filter itself is described in
   section  6.2.2, pdf-page 149, paper-page 175

   The tunning of Alpha and Beta, for using
   the sigmoid as preprocessing for level sets
   is described in section 9.3.3, pdf-page 380,
   paper-page 406.

   Please look at the output of your Sigmoid
   filter. The image should have an appearance
   similar to the one illustrated in Figure 9.16
   in pdf-page 381.  That is, it should look almost
   binarized, with dark regions on the edges of the
   structure that you want to segment, and bright
   values on the inside of the region to be segmented.
   Any bright spots along the edge of the structure
   to be segmented will result in leaks for the
   level set.

   The rule of thumb used for estimating Alpha and
   Beta is described in pdf-page 369.

   The fact that the level set is leaking in your
   example, is an indication that the alpha and beta
   parameters are not tunned correctly.


- Don't bother to run the Geodesic Active Contours
   until you fine tune the output of the Sigmoid
   filter to be a nice looking image.  This image,
   is all what the LevelSet filter sees. Your segmentation
   will be as good or as bad as the feature image that
   you prepare.


- It wasn't clear for me if you were applying these
   process in 3D or 2D. It should work in both ways.
   Once you figure out the parameters, it should be
   simple to run this process in 3D.


- BTW Thanks for sending such detailed description
   of your process. Attaching the images illustrating
   your results is a big help for figuring out the
   potential source of the problem.


-----


You may find useful to play with the application:
GeodesicActiveContour, available in:

    InsightApplications/GeodesicActiveContour

or with the free version of VolView and the ITK
plugin for GeodesicActiveContours. You can download
VolView from:

     http://www . kitware . com/products/volview . html
     http://www . kitware . com/KitwareScripts/download . cgi/volview



Please let us know if you have further question.



  Thanks


    Luis



------------------------------
Christian Dold wrote:
> Hello Mr. Ibanez
> I am using ITK since a couple month to segment the left ventricle of the 
> heart, but the results are not satisfactory.
> The steps I doing with the MRI Images 16 Slices 256x256 resolution:
> Curvature Anisotropic diffusion #of Iterations:10, Time step:0.1, 
> Conductance Parameter: 0.5
> Gradient Magnitude Recursive Gaussian with Sigma: 1
> Sigmoid: Alpha: -0.5 Beta: 1
> Fast Marching: Initial Distance:4 Speed constant:1
> Geodesic Active Contour: Propagation- Curvature- Advection scaling: 1 
> Maximum RMS: 0.02 Maximum Iterations:800
> Binary Treshold: Lower-Upper Value: -1000/0 Outside-Inside Value:0/255
> 
> The result you can see in the attached images. Further the seed points 
> are in the text file.
> 
> I also implemented the Region Growing but no good results.
> Thanks for your suggestions
> Christian
> 
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