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

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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
 
The original pipeline consists of (over a group):  
 
The original pipeline consists of (over a group):  
--preprocessing
+
* preprocessing
---- DTI and FA image calculation, congealing registration of FA images, whole-brain tract seeding, application of registration to tractography,  
+
** DTI and FA image calculation  
 +
** congealing registration of FA images  
 +
** whole-brain tract seeding  
 +
** application of registration to tractography
 +
* 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.
 +
 
 
</div>
 
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<h3>Progress</h3>
 
<h3>Progress</h3>
 
+
* 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
 
</div>
 
</div>
 
</div>
 
</div>
  
 
<div style="width: 97%; float: left;">
 
<div style="width: 97%; float: left;">

Revision as of 17:20, 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
  • 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