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

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:* 4. White matter and gray matter volume creations
 
:* 4. White matter and gray matter volume creations
 
:** Tool: ImageMath
 
:** Tool: ImageMath
:* 5. Genus zero images and surfaces
+
:* 5. Genus zero images and surfaces creation
 
:** Tool: GenusZeroImageFilter (UNC Slicer3 external module)
 
:** Tool: GenusZeroImageFilter (UNC Slicer3 external module)
 
:* 6. Label map creation
 
:* 6. Label map creation
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:* 10. Cortical correspondence on inflated surface
 
:* 10. Cortical correspondence on inflated surface
 
:** Tool: UNC Slicer3 external module
 
:** Tool: UNC Slicer3 external module
 
  
 
=== Usage (Command Line) ===
 
=== Usage (Command Line) ===

Revision as of 18:14, 12 August 2008

Home < 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
  • Workflow for group analysis