Difference between revisions of "DBP2:UNC:Local Cortical Thickness Pipeline"
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Input: T1-weighted image | Input: T1-weighted image | ||
| − | :* 1. Tissue segmentation | + | :* '''1. Tissue segmentation''' |
:** Tool: itkEMS (UNC Slicer3 external module) | :** Tool: itkEMS (UNC Slicer3 external module) | ||
| − | :* 2. Skull stripping | + | :* '''2. Skull stripping''' |
:** Tool: SegPostProcess (UNC Slicer3 external module) | :** Tool: SegPostProcess (UNC Slicer3 external module) | ||
| − | :* 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. White matter and White+Gray matter volume creations | + | :* '''4. White matter and White+Gray matter volume creations''' |
:** Tool: ImageMath | :** Tool: ImageMath | ||
| − | :* 5. Genus zero images and surfaces creation | + | :* '''5. Genus zero images and surfaces creation''' |
:** Tool: GenusZeroImageFilter (UNC Slicer3 external module) | :** Tool: GenusZeroImageFilter (UNC Slicer3 external module) | ||
| − | :* 6. Label map creation | + | :* '''6. Label map creation''' |
:** Tool: ImageMath | :** Tool: ImageMath | ||
| − | :* 7. Laplacian cortical thickness | + | :* '''7. Laplacian cortical thickness''' |
:** Tool: measureThicknessFilter (UNC Slicer3 external module) | :** Tool: measureThicknessFilter (UNC Slicer3 external module) | ||
| − | :* 8. Cortical thickness information on genus zero surface | + | :* '''8. Cortical thickness information on genus zero surface''' |
:** Tool: MeshMath | :** Tool: MeshMath | ||
| − | :* 9. Cortical Surface inflation | + | :* '''9. Cortical Surface inflation''' |
:** Tool: needs to be developped | :** Tool: needs to be developped | ||
| − | :* 10. Cortical correspondence on inflated surface | + | :* '''10. Cortical correspondence on inflated surface''' |
:** Tool: UNC Slicer3 external module | :** Tool: UNC Slicer3 external module | ||
Revision as of 22:31, 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 White+Gray matter volume creations
- Tool: ImageMath
- 5. Genus zero images and surfaces creation
- 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
- Genus zero images and surfaces improvement
- Cortical surface inflation (reading litterature)
Future work
- UNC Slicer3 external modules available on NITRIC
- Workflow for individual analysis (Slicer3 external module using BatchMake)
- Workflow for group analysis
