Difference between revisions of "2010 Winter Project Week WM ATLAS"

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** whole-brain tract seeding  
 
** whole-brain tract seeding  
 
** application of registration to tractography
 
** application of registration to tractography
* EITHER automatic segmentation
+
* EITHER atlas-based segmentation of tractography
** atlas-based segmentation of tractography
 
 
* OR atlas generation
 
* OR atlas generation
 
** clustering of (sample from) whole-brain tractography in group
 
** clustering of (sample from) whole-brain tractography in group
 
** expert labeling of clusters to give anatomical structures
 
** expert labeling of clusters to give anatomical structures
 
** the above produces an atlas that can be used to segment   
 
** the above produces an atlas that can be used to segment   
* analysis
+
* analysis of segmented WM
 
** optimal generation of tract-based coordinate systems per anatomical structure
 
** optimal generation of tract-based coordinate systems per anatomical structure
 
** export of cluster/structure based measurements (FA, etc)
 
** export of cluster/structure based measurements (FA, etc)

Revision as of 17:22, 8 December 2009

Home < 2010 Winter Project Week WM ATLAS

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 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 of segmented WM
    • 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