2010 Winter Project Week WM ATLAS

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  Projects List

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  Automatically segmented fiber tracts.

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  Example whole-brain tract cluster mean fibers.

Key Investigators

• Lauren O'Donnell (Instructor, Harvard Medical School (BWH))
• Carl-Fredrik Westin (Professor, Harvard Medical School (BWH) )
• William Wells (Professor, Harvard Medical School (BWH) )
• Alexandra J Golby (Professor of Neurosurgery, Harvard Medical School (BWH) )

Objective

Implement tract-based morphometry pipeline in 3D Slicer, including atlas-based WM (white matter) segmentation and whole-brain WM coordinate system generation. Investigate integration of FMRI+DTI into atlas pipeline, for neurosurgical planning applications.

Approach, Plan

The original pipeline consists of (over a group):

• preprocessing
  • DTI and FA image calculation
  • congealing registration of FA images
  • whole-brain tract seeding
  • application of registration to tractography
• EITHER automatic segmentation
  • atlas-based segmentation of tractography
• OR atlas generation
  • clustering of (sample from) whole-brain tractography in group
  • expert labeling of clusters to give anatomical structures
  • the above produces an atlas that can be used to segment
• analysis
  • optimal generation of tract-based coordinate systems per anatomical structure
  • export of cluster/structure based measurements (FA, etc)
  • some statistical analysis

The eventual goal is re-implementation of much of the above in the Slicer3 framework. This will enable use of the pipeline for neuroscience research and our future investigation of DTI+fMRI atlases for neurosurgery.

Progress

• Preprocessing
  • work has begun on BatchMake modules for tensor calc and FA calculation in the group
  • some investigation of using congealing implementation in ITK from NAMIC SandBox to replace our current use of original code by Lilla Zollei