[Insight-users] Level set segmentation

[Luis Ibanez]

Hi "Orientation f"

Note that you don't need to *exactly* compute the minimum value
of the gradient magnitude along the contour, nor the mean value
of the gradient magnitude inside the anatomical structure.

     You just need *an estimation* of these two values.

Typically what you can do is to first run a GradientMagnitude
filter in your image, and using any visualization program you
can explore values of the image.

For this purpose you can use

1) the ImageViewer
2) Slicer
3) ParaView

among others....


Any visualization program that allows you to poke at the
pixel values will do the trick.

You could also do it by simply setting up a visualization
program in which you show the output of the Sigmoid at
different values of Alpha and Beta.

See for example:

http://www.itk.org/HTML/FastMarchingLevelSet.htm
http://www.itk.org/HTML/ShapeDetectionLevelSet.htm
http://www.itk.org/HTML/GeodesicActiveContour.htm

and of course SNAP:
http://www.itksnap.org/docs/viewtutorial.php?chapter=TutorialSectionEdgeBasedSegmentation



----


   Regards,


      Luis


--------------------
orientation f wrote:
> Hi
> First, thanks for your help.
> In ITK Software Guide, Alpha and Beta are indicated by K1,K2. But it 
> seems that it's impossible to calculate the minimum value along the 
> contour of the anatomical structure  to be segmented and the average 
> value of the gradient magnitude in the middle of the structure.
> So please give me some advice.
> 
> 2007/10/6, Luis Ibanez <luis.ibanez at kitware.com 
> <mailto:luis.ibanez at kitware.com>>:
> 
> 
>     Hi "orientation f"
> 
>     You will find useful to look at the  FastMarching
>     example application in:
> 
>            InsightApplications/FastMarchingLevelSet
> 
> 
>     This application is described in:
>     http://www.itk.org/HTML/FastMarchingLevelSet.htm
> 
> 
>     You can download the InsightApplications module
>     by following the instruction given in:
> 
>                http://www.itk.org/HTML/Download.php
>     <http://www.itk.org/HTML/Download.php>
> 
> 
>     This application uses FLTK as GUI library (www.fltk.org
>     <http://www.fltk.org>).
> 
> 
>     ---
> 
> 
>     The basic rule of thumb for selecting the parameters of the
>     Sigmoid are given in he ITK Software Guide
> 
>              http://www.itk.org/ItkSoftwareGuide.pdf
> 
>     In Section 9.3.1. "Fast Marching Segmentation",
>     in pdf-pages 565-573.
> 
>     In particular, you will find criteria for finding good values
>     of the Sigmoid parameters Alpha and Beta, in the discussion
>     of K1, K2 values presented at the bottom of pdf-page 569.
> 
> 
>          Regards,
> 
> 
> 
>              Luis
> 
> 
> 
>     ---------------------
>     orientation f wrote:
>      > Hello
>      > I want to segment DICOM image with level set methods ,such as fast
>      > marching. It is difficult to set its parameters, especilly the
>      > parameters of  Sigmoid function( sigmoid->setAlpha(),
>      > sigmoid->SetBeta()). it will be thankful if you can tell me,
>     according
>      > specified image, how to obtain the value of Alpha and Beta!
>      > please give me a simple example of itk+vtk+mfc if you have any.
>      > thanks!
>      >
>      >
>      >
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