[Insight-users] Semiautomatic liver segmentation

[Luis Ibanez]

Hi Ivan,

We have experience ITK segmentation methods for liver
segmentation but using CT instead of MRI. The methods
that are well suited for this problem are:

   1) Watersheds
   2) LevelSets

Region growing methods are good as a first try and can
be used as initializers for the LevelSets methods. The
problem with region growing methods is that they don't
have any notion of "shape", so, it is enough to have
one single badly connected pixel and all the region
will leak.

LevelSets on the other hand allow to represent the
notion of shape by controlling the curvature.


Before encoding all this by yourself you should probably
play with:

A) The segmentation editor application (in InsightApplications)
    There is a new FLTK based version. It will allow you to
    navigate through the watershed hierarchy and get an idea of
    the suitability of the segmentation.

B) VolView has a set of plugins for level sets. In particular
    FastMarching, ShapeDetection and GeodesicActive contours.
    The later is probably the best adapted for this problem
    since you can control curvature.


If you can make an example dataset available we could be able
to give it a try and provide you more detailed advice.


Regards,


   Luis



--------------------
Ivan Macia wrote:
> Dear ITK users
> 
> Im working on a semiautomatic segmentation of the liver surface using MRI
> images. Im trying to test several segmentation methods using the algorithms
> available in ITK.
> 
> One of the approaches I have taken is using the Neighborhood Connected
> Threshold filter to segment the liver after a first preprocessing of the
> image using Curvature Flow filter. The results are reasonably good but still
> the segmentation result includes many areas outside the liver region. There
> is also the difficulty of selecting the thresholds for the Neighborhood
> filter due to the variability of the intensities with MRI images.
> 
> I am currently working in the implementation of Geodesic Active Contours
> following the pipeline in the ITK guide. I am also thinking in trying
> Watershed filter.
> 
> Has anyone had experience with liver segmentation with MRI? I have seen that
> there is an ITK project going on about this.  I would like to know, if
> possible, which methods or preprocessing steps have given good results or
> any good reference to the topic.
> 
> Thank you very much in advance for your help
> 
> Ivan Macia
> 
> __________________________________
> Ivan Macia
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