Difference between revisions of "DBP2:UNC:Local Cortical Thickness Pipeline"
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(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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:* 3. Atlas-based structures segmentation: subcortical structures, cerebellum, lateral ventricles | :* 3. Atlas-based structures segmentation: subcortical structures, cerebellum, lateral ventricles | ||
:** 3.1 Deformable registration of T1-weighted pediatric atlas | :** 3.1 Deformable registration of T1-weighted pediatric atlas | ||
| − | :***Tool: RegisterImages (Slicer3 module) | + | :***Tool: RegisterImages (Slicer3 module) |
:** 3.2. Applying transformations to the structures | :** 3.2. Applying transformations to the structures | ||
:*** Tool: ResampleVolume2 (Slicer3 module) | :*** Tool: ResampleVolume2 (Slicer3 module) | ||
| − | :* 4. | + | :* 4. White matter and gray matter volume creations |
| − | :** Tool: | + | :** Tool: ImageMath |
:* 5. Genus zero images and surfaces | :* 5. Genus zero images and surfaces | ||
| − | :** Tool: | + | :** Tool: GenusZeroImageFilter (UNC Slicer3 external module) |
:* 6. Label map creation | :* 6. Label map creation | ||
| − | :** Tool: | + | :** Tool: ImageMath |
:* 7. Laplacian cortical thickness | :* 7. Laplacian cortical thickness | ||
| − | :** Tool: | + | :** Tool: measureThicknessFilter (UNC Slicer3 external module) |
| + | :* 8. Cortical thickness information on genus zero surface | ||
| + | :** Tool: MeshMath | ||
| + | :* 9. Cortical Surface inflation | ||
| + | :** Tool: needs to be developped | ||
| + | :* 10. Cortical correspondence on inflated surface | ||
| + | :** Tool: UNC Slicer3 external module | ||
| + | |||
=== Usage (Command Line) === | === Usage (Command Line) === | ||
Revision as of 18:01, 12 August 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
- 1. Tissue segmentation
- Tool: itkEMS (UNC Slicer3 external module)
- 2. Skull stripping
- Tool: SegPostProcess (UNC Slicer3 external module)
- 3. Atlas-based structures segmentation: subcortical structures, cerebellum, lateral ventricles
- 3.1 Deformable registration of T1-weighted pediatric atlas
- Tool: RegisterImages (Slicer3 module)
- 3.2. Applying transformations to the structures
- Tool: ResampleVolume2 (Slicer3 module)
- 3.1 Deformable registration of T1-weighted pediatric atlas
- 4. White matter and gray matter volume creations
- Tool: ImageMath
- 5. Genus zero images and surfaces
- Tool: GenusZeroImageFilter (UNC Slicer3 external module)
- 6. Label map creation
- Tool: ImageMath
- 7. Laplacian cortical thickness
- Tool: measureThicknessFilter (UNC Slicer3 external module)
- 8. Cortical thickness information on genus zero surface
- Tool: MeshMath
- 9. Cortical Surface inflation
- Tool: needs to be developped
- 10. 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
Future work
- UNC Slicer3 external modules available on NITRIC
- Workflow for individual analysis
- Workflow for group analysis
