Difference between revisions of "2008 Summer Project Week:RegionalCorticalThicknessTool"

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Our plan for the project week is to start the development of a work flow tool allowing regional cortical thickness analysis.  
 
Our plan for the project week is to start the development of a work flow tool allowing regional cortical thickness analysis.  
 
Pipeline:
 
Pipeline:
- Tissue segmentation: itkEMSCLP UNC external Slicer3 module
+
* Tissue segmentation: itkEMSCLP (UNC external Slicer3 module)
- Skull Stripping: in progress (UNC Slicer3 external modules) - ImageMath and SegPostProcess Slicer3 modules
+
* Skull Stripping: ImageMath and SegPostProcess (UNC Slicer3 external modules) - in progress
- Lobar parcellation registration
+
* Lobar parcellation registration
  - Atlas to case affine registration: AffineRegistration module
+
** Atlas to case affine registration: AffineRegistration module
  - Atlas to case BSPline registration: Deformable BSpline registration module
+
** Atlas to case BSpline registration: Deformable BSpline registration module
  - Applying transformation to parcellation map: Resample Volume 2 module
+
** Applying transformation to parcellation map: Resample Volume 2 module
- Cortical Thickness: CortthickCLP (UNC Slicer3 external module)
+
* Cortical Thickness: CortthickCLP (UNC Slicer3 external module)
 
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<h1>Progress</h1>
 
<h1>Progress</h1>
 
Attended:
 
Attended:
- Special topic breakout: Non-rigid registration
+
* Special topic breakout: Non-rigid registration (interested in RegisterImages module)
- Special topic breakout: GWE
+
* Special topic breakout: GWE
  
 +
The regional cortical thickness workflow has been developped using the module chaining method (Help from Marco Ruiz).
 +
One part of the pipeline needs to be continued (skull stripping step)
  
 
</div>
 
</div>

Latest revision as of 18:56, 30 June 2008

Home < 2008 Summer Project Week:RegionalCorticalThicknessTool



Key Investigators

  • UNC: Heather Cody Hazlett, Martin Styner, Clement Vachet
  • GE: Jim Miller


Objective

We would like to create an end-to-end application within Slicer3 allowing individual and group analysis of regional and local cortical thickness.

Such a workflow applied to the young brain (2-4 years old) is our goal in order to start a longitudinal study of early brain development in autism (UNC DBP).

See our Roadmap for more details.

Approach, Plan

Our plan for the project week is to start the development of a work flow tool allowing regional cortical thickness analysis. Pipeline:

  • Tissue segmentation: itkEMSCLP (UNC external Slicer3 module)
  • Skull Stripping: ImageMath and SegPostProcess (UNC Slicer3 external modules) - in progress
  • Lobar parcellation registration
    • Atlas to case affine registration: AffineRegistration module
    • Atlas to case BSpline registration: Deformable BSpline registration module
    • Applying transformation to parcellation map: Resample Volume 2 module
  • Cortical Thickness: CortthickCLP (UNC Slicer3 external module)

Progress

Attended:

  • Special topic breakout: Non-rigid registration (interested in RegisterImages module)
  • Special topic breakout: GWE

The regional cortical thickness workflow has been developped using the module chaining method (Help from Marco Ruiz). One part of the pipeline needs to be continued (skull stripping step)