Difference between revisions of "2010 Winter Project Week WM ATLAS"
From NAMIC Wiki
| Line 24: | Line 24: | ||
<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 | |
| − | + | ** 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> | </div> | ||
| Line 31: | Line 47: | ||
<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
Automatically segmented fiber tracts.
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
- 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
