[Insight-users] Segmentation editor?

[Luis Ibanez]

Hi Yasser,

Unfortunately there is no a single segmentation method
that will work for any anatomical structure and any
image modality. The effectiveness of segmentation
depends on the characteristics of your image.


Here are the basic questions you may have to ask before
starting:

1) What anatomical structures do you want to segment ?
2) How homogeneous are the fields of your MRIs ?
3) What are the typical values of pixel spacing in your volumes?
4) What is the noise level of the image ?


Good ITK applications to start playing with your volumes
are the following:

1) RegionGrowingSegmentation,
    available in
    InsightApplications/RegionGrowingSegmentation
    It requires ITK, FLTK and VTK.
    http://www.itk.org/HTML/RegionGrowingSegmentation.htm

2) SegmentationEditor
    available in
    InsightApplications/SegmentationEditor
    It applies watersheds for segmenting the image.
    It requires ITK and VTK (with Tcl wrapping).
    http://www.itk.org/HTML/WatershedSegmentationExample.html

    a more recent version is available in
    InsightApplications/SegmentationEditorFltkGui
    This version uses FLTK instead of Tcl as GUI support.

3) FastMarchingLevelSet
    available in
    InsightApplications/FastMarchingLevelSet
    It allows to run FastMarching from a set of user provided seeds.
    It requires ITK + FLTK + VTK
    http://www.itk.org/HTML/FastMarchingLevelSet.htm

4) ShapeDetectionLevelSet
    available in
    InsightApplications/ShapeDetectionLevelSet
    uses a FastMarching initialization followed by a shape detection
    level set filter. It requires ITK + FLTK + VTK
    http://www.itk.org/HTML/ShapeDetectionLevelSet.htm

5) GeodesicActiveContour
    available in
    InsightApplications/GeodesicActiveContour
    it requires ITK + FLTK + VTK
    initialize a level set with FastMarching and then
    applies a GeodesicActiveContour
    http://www.itk.org/HTML/GeodesicActiveContour.htm

6) Morphogenesis
    available in
    InsightApplications/Morphogenesis
    it requriees ITK + FLTK
    It simulates the growth of a cellular aggregate (e.g. bacteria)
    for segmenting a region of the image.
    http://www.itk.org/HTML/Morphogenesis.htm



I would suggest you to start with RegionGrowing first and then
move to the LevelSet methods if region growig doesn't work as
you want.


The principles on which all these applications are based
are described in the ITK SoftwareGuide:

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

You may want to get some coffee read carefully the
chapter on segmentation.

----

If you want to use VTK with ITK you have to build VTK
by yourself and configure it correctly with CMake.
Please post to the list any difficulties you may
encounter.



   Regards,


    Luis


---------------------
yasser salman wrote:
> hi luis..,
> i need to segment a series of MRI slices ,View and save it what is the best application can i start from? Is it a segmentation editor?
> if i need to build a segmentation editor.., i already built ITK with CMake and it's ok.., FLTK and it's ok , but VTK not build in cmake (i use it in VC++ with include header only).., what can i do ?
> 
> regard's
> yasser..,
> 
>