Difference between revisions of "DBP2:UNC:Regional Cortical Thickness Pipeline"
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We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness. | We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional cortical thickness. | ||
| − | == Pipeline description (steps) == | + | == General information == |
| + | |||
| + | === Pipeline description (steps) === | ||
Input: T1-weighted image | Input: T1-weighted image | ||
| Line 23: | Line 25: | ||
| − | == Usage (Command Line) == | + | === Usage (Command Line) === |
Input: | Input: | ||
| Line 37: | Line 39: | ||
| − | == Analysis on a small pediatric dataset == | + | === Analysis on a small pediatric dataset === |
Tests have been computed on a small pediatric dataset, including 2 years old and 4 years old cases | Tests have been computed on a small pediatric dataset, including 2 years old and 4 years old cases | ||
| Line 45: | Line 47: | ||
| − | == In progress == | + | === In progress === |
| − | :* Workflow for individual analysis | + | :* Workflow for individual analysis (Slicer3 external module using BatchMake) |
| − | == Future work == | + | === Future work === |
:* UNC Slicer3 external modules available on NITRIC | :* UNC Slicer3 external modules available on NITRIC | ||
| + | :* pediatric atlas available to the community (XNAT?) | ||
:* Workflow for group analysis | :* Workflow for group analysis | ||
Revision as of 16:27, 12 August 2008
Home < DBP2:UNC:Regional Cortical Thickness PipelineBack 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.
General information
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
Tests have been computed on a small pediatric dataset, including 2 years old and 4 years old cases
- 2 Autistic cases
- 1 developmental delay
- 1 normal control
In progress
- Workflow for individual analysis (Slicer3 external module using BatchMake)
Future work
- UNC Slicer3 external modules available on NITRIC
- pediatric atlas available to the community (XNAT?)
- Workflow for group analysis
