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

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We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of local cortical thickness.
 
We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of local cortical thickness.
  
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== General information ==
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<center>
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{|
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|[[Image:T1Image.jpg|thumb|250px|T1-weighted skull-stripped image]]
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|valign="center"|[[Image:Parcellation.jpg|thumb|250px|Parcellation image]]
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|valign="center"|[[Image:WMThickness.jpg|thumb|250px|Cortical thickness on WM surface]]
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|valign="center"|[[Image:ThicknessInformation.jpg|thumb|250px|Cortical thickness information]]
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|}
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</center>
  
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=== Pipeline description (steps) ===
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== Pipeline overview ==
  
 
Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)
 
Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)
  
 
:* '''1. Tissue segmentation'''
 
:* '''1. Tissue segmentation'''
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:** Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
 
:** Tool: itkEMS (UNC Slicer3 external module)
 
:** Tool: itkEMS (UNC Slicer3 external module)
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:* '''2. Atlas-based ROI segmentation:''' subcortical structures, lateral ventricles, cerebellum
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:* '''2. Atlas-based ROI segmentation:''' subcortical structures, lateral ventricles, parcellation
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:** 2.1 Deformable registration of T1-weighted pediatric atlas
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:** 2.1 T1-weighted atlas deformable registration
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:***Tool: RegisterImages (Slicer3 module)
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:*** B-spline pipeline registration
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:*** Tool: RegisterImages (Slicer3 module)
 
:** 2.2. Applying transformations to the structures
 
:** 2.2. Applying transformations to the structures
 
:*** Tool: ResampleVolume2 (Slicer3 module)
 
:*** Tool: ResampleVolume2 (Slicer3 module)
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:* '''3. White matter map and gray matter map images creation'''
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:* '''3. White matter map creation'''
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:** Brainstem and cerebellum extraction
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:** Adding subcortical structures except amygdala and hippocampus
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:** Tool: ImageMath (NTIRC module)
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:* '''4. White matter map post-processing'''
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:** Largest component computation
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:** White matter filling
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:** Smoothing: Level set smoothing or weighted average filter
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:** Connectivity enforcement (6-connectivity)
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:** Tool: SegPostProcessB (Slicer3 external module)
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:* '''5. Genus zero white matter map image and surface creation'''
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:** Tool: GenusZeroImageFilter (UNC Slicer3 external module)
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:* '''6. Gray matter map creation'''
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:** Adding genus zero white matter map to gray matter segmentation (without cerebellum and brainstem)
 
:** Tool: ImageMath
 
:** Tool: ImageMath
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:* '''4. Genus zero images and surfaces creation'''
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:* '''7. White matter surface inflation'''
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:** Tool: GenusZeroImageFilter (UNC Slicer3 external module)
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:** Tool: MeshInflation (UNC Slicer3 external module)
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:* '''5. Label map creation'''
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:* '''8. Cortical correspondence'''
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:** Correspondence on inflated surface using particle system
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:** Tool: ParticleCorrespondence (UNC Slicer3 external module)
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:* '''9. Label map creation'''
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:** Label map creation for cortical thickness computation (WM + GM + "CSF")
 
:** Tool: ImageMath
 
:** Tool: ImageMath
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:* '''6. Laplacian cortical thickness'''
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:* '''10. Cortical thickness'''
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:** Tool: measureThicknessFilter (UNC Slicer3 external module)
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:** Asymmetric local cortical thickness or Laplacian cortical thickness
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:* '''7. Cortical thickness information on genus zero surface'''
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:** Tool: UNCCortThick or measureThicknessFilter (UNC Slicer3 external modules)
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:** Tool: CompCortThick (based on Danielsson map)
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:* '''11. Group statistical analysis'''
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:* '''8. Cortical Surface inflation'''
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:** Tool: QDEC Slicer module or StatNonParamPDM
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:** Tool: MeshInflation -- in progress --
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:* '''9. Cortical correspondence on inflated surface'''
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== Download ==
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:** Tool: UNC Slicer3 external module
 
  
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=== Usage (Command Line) ===
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=== Usage ===
  
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needs to be done
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=== Command line execution ===
  
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=== Step by step command line execution ===
  
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=== Analysis on a small pediatric dataset ===
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== Pipeline validation ==
  
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needs to be done
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== Planning ==
  
 
=== In progress ===
 
=== In progress ===
  
 
:* Cortical surface inflation: module in progress  
 
:* Cortical surface inflation: module in progress  
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:** Iterative smoothing using relaxation operator (considering average vertex) and L2 norm of the mean curvature as a stopping criterion
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:* Iterative smoothing using relaxation operator (considering average vertex) and L2 norm of the mean curvature as a stopping criterion
  
 
=== Future work ===
 
=== Future work ===

Revision as of 00:28, 14 December 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.

T1-weighted skull-stripped image
Parcellation image
Cortical thickness on WM surface
Cortical thickness information

Pipeline overview

Input: RAW images (T1-weighted, T2-weighted, PD-weighted images)

  • 1. Tissue segmentation
    • Probabilistic atlas-based automatic tissue segmentation via an Expectation-Maximization scheme
    • Tool: itkEMS (UNC Slicer3 external module)
  • 2. Atlas-based ROI segmentation: subcortical structures, lateral ventricles, parcellation
    • 2.1 T1-weighted atlas deformable registration
      • B-spline pipeline registration
      • Tool: RegisterImages (Slicer3 module)
    • 2.2. Applying transformations to the structures
      • Tool: ResampleVolume2 (Slicer3 module)
  • 3. White matter map creation
    • Brainstem and cerebellum extraction
    • Adding subcortical structures except amygdala and hippocampus
    • Tool: ImageMath (NTIRC module)
  • 4. White matter map post-processing
    • Largest component computation
    • White matter filling
    • Smoothing: Level set smoothing or weighted average filter
    • Connectivity enforcement (6-connectivity)
    • Tool: SegPostProcessB (Slicer3 external module)
  • 5. Genus zero white matter map image and surface creation
    • Tool: GenusZeroImageFilter (UNC Slicer3 external module)
  • 6. Gray matter map creation
    • Adding genus zero white matter map to gray matter segmentation (without cerebellum and brainstem)
    • Tool: ImageMath
  • 7. White matter surface inflation
    • Tool: MeshInflation (UNC Slicer3 external module)
  • 8. Cortical correspondence
    • Correspondence on inflated surface using particle system
    • Tool: ParticleCorrespondence (UNC Slicer3 external module)
  • 9. Label map creation
    • Label map creation for cortical thickness computation (WM + GM + "CSF")
    • Tool: ImageMath
  • 10. Cortical thickness
    • Asymmetric local cortical thickness or Laplacian cortical thickness
    • Tool: UNCCortThick or measureThicknessFilter (UNC Slicer3 external modules)
  • 11. Group statistical analysis
    • Tool: QDEC Slicer module or StatNonParamPDM

Download

Usage

Command line execution

Step by step command line execution

Pipeline validation

Planning

In progress

  • Cortical surface inflation: module in progress
  • Iterative smoothing using relaxation operator (considering average vertex) and L2 norm of the mean curvature as a stopping criterion

Future work

  • UNC Slicer3 external modules available on NITRIC
  • Workflow for individual analysis (Slicer3 external module using BatchMake)
  • Workflow for group analysis
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