DBP2:UNC:Local Cortical Thickness Pipeline
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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: RAW images (T1-weighted, T2-weighted, PD-weighted images)
- 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: CompCortThick (based on Danielsson map)
- 8. Cortical Surface inflation
- Tool: MeshInflation -- 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
- Cortical surface inflation: module in progress
- Iterative smoothing using relaxation operator (considering average vertex) and L2 norm of the mean curvature as a stopping criterion
- 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