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)