Difference between revisions of "DBP2:UNC:Local Cortical Thickness Pipeline"
From NAMIC Wiki
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:* '''1. Tissue segmentation''' | :* '''1. Tissue segmentation''' | ||
:** Tool: itkEMS (UNC Slicer3 external module) | :** Tool: itkEMS (UNC Slicer3 external module) | ||
| − | :* '''2 | + | :* '''2. Atlas-based ROI segmentation:''' subcortical structures, lateral ventricles, cerebellum |
| − | + | :** 2.1 Deformable registration of T1-weighted pediatric atlas | |
| − | |||
| − | :** | ||
:***Tool: RegisterImages (Slicer3 module) | :***Tool: RegisterImages (Slicer3 module) | ||
| − | :** | + | :** 2.2. Applying transformations to the structures |
:*** Tool: ResampleVolume2 (Slicer3 module) | :*** Tool: ResampleVolume2 (Slicer3 module) | ||
| − | :* ''' | + | :* '''3. White matter map and gray matter map images creation''' |
:** Tool: ImageMath | :** Tool: ImageMath | ||
| − | :* ''' | + | :* '''4. Genus zero images and surfaces creation''' |
:** Tool: GenusZeroImageFilter (UNC Slicer3 external module) | :** Tool: GenusZeroImageFilter (UNC Slicer3 external module) | ||
| − | :* ''' | + | :* '''5. Label map creation''' |
:** Tool: ImageMath | :** Tool: ImageMath | ||
| − | :* ''' | + | :* '''6. Laplacian cortical thickness''' |
:** Tool: measureThicknessFilter (UNC Slicer3 external module) | :** Tool: measureThicknessFilter (UNC Slicer3 external module) | ||
| − | :* ''' | + | :* '''7. Cortical thickness information on genus zero surface''' |
:** Tool: MeshCortThick | :** Tool: MeshCortThick | ||
| − | :* ''' | + | :* '''8. Cortical Surface inflation''' |
:** Tool: needs to be developped | :** Tool: needs to be developped | ||
| − | :* ''' | + | :* '''9. Cortical correspondence on inflated surface''' |
:** Tool: UNC Slicer3 external module | :** Tool: UNC Slicer3 external module | ||
Revision as of 21:15, 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. 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: needs to be developped
- 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 (reading litterature)
Future work
- UNC Slicer3 external modules available on NITRIC
- Workflow for individual analysis (Slicer3 external module using BatchMake)
- Workflow for group analysis
