2008 Summer Project Week:RegionalCorticalThicknessTool

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Home < 2008 Summer Project Week:RegionalCorticalThicknessTool

Key Investigators

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


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)



  • 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)