NA-MIC/Projects/Structural/Segmentation/Rule based segmentation:Striatum

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Objective: Semi Automatic Segmentation and parcellation for the Basal Ganglia.

Progress: We have developed an algorithm for delineation of the striatum into 5 physiological subregions (pre/post caudate, pre/post putamen, and nucleus accumbens) while requiring only minimal user input. We have implemented this algorithm from the geometric rules for delineating the striatum as defined by our Core 3 collaborator, Dr. James Levitt of the PNL, into a 3D SLICER module. The current run time for the algorithm is ~20 seconds after the initial user input. The user inputs a label map of the full striatum, the most superior/dorsal voxel of the putamen on each slice, and the anterior commisure voxel (see figure below). From these, the labelmap is delineated into the aforementioned subregions. The figure below shows a 3D model of the left and right striatum delineated into the five subregions.


Key Investigators:

  • GTech: Ramsey Al-Hakim, Delphine Nain, Allen Tannenbaum.
  • PNL: Sylvain Bouix, James Levitt, Marc Niethammer, Martha Shenton.
  • Kitware: Luis Ibanez
  • Isomics: Steve Pieper