Shape Segmentation

Slicer extension for automatic segmentation of surface meshes (assigning labels to the triangles). The underlying algorithm uses graph partitioning based on the "shape diameter function" from CGAL.

Installation

The extension have not been packaged yet, so compile manually using cmake, which requires a superbuild of Slicer. Remember to change the Slicer path in the instructions below. It further depends on CGAL which must be installed and available for cmake.

git clone https://github.com/spietz/SlicerShapeSegmentation.git
mkdir SlicerShapeSegmentation/build
cd SlicerShapeSegmentation/build
cmake DSlicer_DIR:PATH=/home/user/Slicer-SuperBuild-Debug/Slicer-build -DCMAKE_BUILD_TYPE=Release ..
make

Once compiled add it to Slicer by browsing to the directory of 'ShapeSegmentation/build/lib/Slicer-*/cli-modules' when clicking 'Edit->Application Settings->Modules->Additional module paths->Add'.

References

• CGAL documentation on surface segmentation and references therein.

TODO

• Add parameters for computing the shape diameter function.
• Compute shape diameter function seperately from segmentation.
• Allow any scalar field to guide the segmentation.
• Convert surface labels to volumetric label map to edit with the Segment Editor.
• Package extension for use without Slicer superbuild.