DBP2:UNC:Regional 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 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)

All the tools used in the current pipeline are Slicer3 modules, some of them being UNC external modules. Thus, the user can process a data and compute a cortical thickness regional analysis, either using Slicer3 GUI modules or by command lines tools

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 (T1-weighted image and parcellation map) available to the community (XNAT?)
• Workflow for group analysis (KWWidget application using BatchMake)