Difference between revisions of "DBP2:UNC:Regional Cortical Thickness Pipeline"

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(New page: Back to UNC Cortical Thickness Roadmap __NOTOC__ == Objective == We would like to create an end-to-end application within Slicer3 allowing indiv...)
 
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== Analysis on a small pediatric dataset ==
 
== Analysis on a small pediatric dataset ==
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Tests have been computed on a small pediatric dataset, including 2 years old and 4 years old cases
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:* 2 Autistic cases
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:* 1 developmental delay
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:* 1 normal control
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== In progress ==
 
== In progress ==

Revision as of 16:22, 12 August 2008

Home < 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.

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:

  • 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

Future work

  • UNC Slicer3 external modules available on NITRIC
  • Workflow for group analysis