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Hierarchical Model of the EMSegmenter


This module is designed for users who perform atlas based medical image segmentation.


The Slicer4 version of the EMSegmenter is still under development. A major change will be that the EMSegmenter will not be included into Slicer4 base but will be available as a downloadable extension. This was necessary due to the growing size of the EMS package.

Also, the EMSegmenter will use the same repository for Slicer3 and Slicer4 versions to enhance maintenance for users and developers. The base code will is available in the Slicer3 trunk. To checkout the Slicer4 extension, a checkout on a sub-directory has to be performed (see installation instructions below). This has the advantage that the logic and algorithm classes are shared between Slicer3 and Slicer4 and only the GUI changes depending on the Slicer version.

Another change is that the 3D Slicer4 EMSegment Wizard is written in Python. This results in very clean code. The algorithm and computing classes are still in C++ for performance.


The Slicer4 version of the EMSegmenter can be installed as follows until the extension infrastructure is realized in Slicer4:

   svn co EMSegment4
   mkdir EMSegment4-build
   cd EMSegment4-build
   ccmake -DSlicer_DIR:PATH=/path/to/Slicer4-Superbuild/Slicer-build ../EMSegment4
   make -j 4
   /path/to/Slicer4-Superbuild/Slicer-build/Slicer --add-loadable-extension-path EMSegment4 "/path/to/EMSegment4-build"

Please note that the module is still under heavy development.

General Features

Porting this module to Slicer4 is in progress. To compare the GUI elements between slicer3 and slicer4 click here