[Insight-users] Problems on using the GeodesicActiveContourSegmentation Application

[Luis Ibanez]

Hi Kai,

Here are the parameters that you can use
with the GeodesicActiveContourSegmentation
application (in InsightApplications), in
order to segment the ventricles from one
of the BrainWeb datasets.


1) Load the BrainWeb image:

         brainweb1e1a10f20.mha

2) In FastMarching
    2.1) Set the distance to 3.0
    2.2) Set Stopping value = 10.0

4) In Gradient magnitude keep sigma = 1.2

5) In Sigmoid keep alpha = -1, beta= 5.0

6) In GeodesicActive contour do:

    6.1) RMS error  = 0.01
    6.2) Iterations = 200
    6.3) Curvature scaling   =  1.0
    6.4) Propagation scaling = 20.0
    6.5) Advection scaling   = 20.0

7) Place seed point at locations
    (or close to them)

    7.1)   ( 67,  87,  87)
    7.2)   (113,  87,  87)
    7.3)   ( 85, 135,  87)
    7.4)   ( 95, 135,  87)
    7.5)   ( 78, 108,  97)
    7.6)   (101, 108,  97)


The reason why you may be getting always
a sphere is that the weight of propagation
and advection terms are too low in your
case, so the front is not moving enough.

The VTK visualization button is something
that was never finished in this application.
So it is normal (although it is not good)
that the displayed window is all white.

If you really want to see a volume rendering
of the resulting segmentation, is is much
easier now to use VolView and  its ITK Geodesic
Active Contour plugin.  You can download the
free version of VolView from:

http://www.kitware.com/products/volview.html

--

------------------------------------
IMAGINE: If one day published papers
will have all the source code, data
and the parameters needed in order
to reproduce results...
------------------------------------



   Luis




--------------
Kai Li wrote:

> Hi,
>   I tried the GeodesicActiveContourSegmentation application for a brainweb
> dataset. It seems to work fine with segmentation of white matter. But I
> haven't made it work with ventricles. What I did was just putting a seed
> point within a ventricle and leave all parameters default except for the
> distance of FastMarching filter,  the RMS error and iterations of the
> GeodesicActiveContour filter. I set the distance of the FastMarching
> filter to be just "1.0". The problem is that no matter how I decrease the
> RMS error and increase the iterations, the result is always a small sphere
> like shape around the seed point.
> 
>  Another problem is about the VTK Render. After the Threshhold filter is
> executed, the color in the "VTK Render" button is still red. If I click
> on the button, I just get a blank window. The fltkImageViewer(the
> "Display" button) works fine though. I think I have succesfully installed
> the VTK library.
> 
>  Any help is highly appreciated.
> 
> Kai
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