Difference between revisions of "DBP2:UNC:Local Cortical Thickness Pipeline"
From NAMIC Wiki
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:** Tool: MeshCortThick | :** Tool: MeshCortThick | ||
:* '''8. Cortical Surface inflation''' | :* '''8. Cortical Surface inflation''' | ||
| − | :** Tool: | + | :** Tool: in progress |
:* '''9. Cortical correspondence on inflated surface''' | :* '''9. Cortical correspondence on inflated surface''' | ||
:** Tool: UNC Slicer3 external module | :** Tool: UNC Slicer3 external module | ||
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:* Genus zero images and surfaces improvement | :* Genus zero images and surfaces improvement | ||
| − | :* Cortical surface inflation | + | :* Cortical surface inflation: module in progress |
=== Future work === | === Future work === | ||
Revision as of 20:17, 17 October 2008
Home < DBP2:UNC:Local 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 local cortical thickness.
General information
Pipeline description (steps)
Input: T1-weighted image, T2-weighted image, PD-weighted image
- 1. Tissue segmentation
- Tool: itkEMS (UNC Slicer3 external module)
- 2. Atlas-based ROI segmentation: subcortical structures, lateral ventricles, cerebellum
- 2.1 Deformable registration of T1-weighted pediatric atlas
- Tool: RegisterImages (Slicer3 module)
- 2.2. Applying transformations to the structures
- Tool: ResampleVolume2 (Slicer3 module)
- 2.1 Deformable registration of T1-weighted pediatric atlas
- 3. White matter map and gray matter map images creation
- Tool: ImageMath
- 4. Genus zero images and surfaces creation
- Tool: GenusZeroImageFilter (UNC Slicer3 external module)
- 5. Label map creation
- Tool: ImageMath
- 6. Laplacian cortical thickness
- Tool: measureThicknessFilter (UNC Slicer3 external module)
- 7. Cortical thickness information on genus zero surface
- Tool: MeshCortThick
- 8. Cortical Surface inflation
- Tool: in progress
- 9. Cortical correspondence on inflated surface
- Tool: UNC Slicer3 external module
- 1. Tissue segmentation
Usage (Command Line)
needs to be done
Analysis on a small pediatric dataset
needs to be done
In progress
- Genus zero images and surfaces improvement
- Cortical surface inflation: module in progress
Future work
- UNC Slicer3 external modules available on NITRIC
- Workflow for individual analysis (Slicer3 external module using BatchMake)
- Workflow for group analysis
