DBP2:UNC:Regional 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 regional 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. Deformable registration of pediatric regional atlas
    • 3.1 Deformable registration of T1-weighted pediatric atlas
      • Tool: RegisterImages (Slicer3 module)
    • 3.2. Applying transformation to the parcellation map
      • Tool: ResampleVolume2 (Slicer3 module)
  • 4. Cortical Thickness
    • Tool: CortThick (UNC Slicer3 module)


Usage (Command Line)

Input T1_weighted image: Input T1-weigthed atlas: Input regional atlas (parcellation map):

  • 1. Tissue segmentation
  • 2. Skull stripping
  • 3. Deformable registration of pediatric regional atlas
    • 3.1 Deformable registration of T1-weighted pediatric atlas
    • 3.2. Applying transformation to the parcellation map
  • 4. Cortical Thickness


Analysis on a small pediatric dataset

Tests have been computed on a small pediatric dataset, including 2 years old and 4 years old cases

  • 2 Autistic cases
  • 1 developmental delay
  • 1 normal control


In progress

  • Workflow for individual analysis (Slicer3 external module using BatchMake)

Future work

  • UNC Slicer3 external modules available on NITRIC
  • pediatric atlas available to the community (XNAT?)
  • Workflow for group analysis