DBP2:UNC:Regional Cortical Thickness Pipeline
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Revision as of 16:15, 12 August 2008 by Cvachet (talk | contribs) (New page: Back to UNC Cortical Thickness Roadmap __NOTOC__ == Objective == We would like to create an end-to-end application within Slicer3 allowing indiv...)
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Back to UNC Cortical Thickness Roadmap
Objective
We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness.
Pipeline description (steps)
Input: T1-weighted image
- 1. Tissue segmentation
- Tool: itkEMS (UNC Slicer3 external module)
- 2. Skull stripping
- Tool: SegPostProcess (UNC Slicer3 external module)
- 3. Deformable registration of pediatric regional atlas
- 3.1 Deformable registration of T1-weighted pediatric atlas
- Tool: RegisterImages (Slicer3 module)
- 3.2. Applying transformation to the parcellation map
- Tool: ResampleVolume2 (Slicer3 module)
- 3.1 Deformable registration of T1-weighted pediatric atlas
- 4. Cortical Thickness
- Tool: CortThick (UNC Slicer3 module)
- 1. Tissue segmentation
Usage (Command Line)
Input:
- 1. Tissue segmentation
- 2. Skull stripping
- 3. Deformable registration of pediatric regional atlas
- 3.1 Deformable registration of T1-weighted pediatric atlas
- 3.2. Applying transformation to the parcellation map
- 4. Cortical Thickness
- 3. Deformable registration of pediatric regional atlas
Analysis on a small pediatric dataset
In progress
- Workflow for individual analysis
Future work
- UNC Slicer3 external modules available on NITRIC
- Workflow for group analysis
