Difference between revisions of "DBP2:UNC:Local Cortical Thickness Pipeline"
From NAMIC Wiki
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=== Pipeline description (steps) === | === Pipeline description (steps) === | ||
| − | Input: T1-weighted image | + | Input: T1-weighted image, T2-weighted image, PD-weighted image |
:* '''1. Tissue segmentation''' | :* '''1. Tissue segmentation''' | ||
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:** 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 | + | :* '''4. White matter and White+Gray matter volumes creation''' |
:** Tool: ImageMath | :** Tool: ImageMath | ||
:* '''5. Genus zero images and surfaces creation''' | :* '''5. Genus zero images and surfaces creation''' | ||
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:** 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: | + | :** Tool: MeshCortThick |
:* '''9. Cortical Surface inflation''' | :* '''9. Cortical Surface inflation''' | ||
:** Tool: needs to be developped | :** Tool: needs to be developped | ||
Revision as of 20:53, 19 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, T2-weighted image, PD-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 volumes creation
- 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: MeshCortThick
- 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
