DBP2:UNC:Local Cortical Thickness Pipeline

Back 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)
• 4. White matter and 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

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