Difference between revisions of "2008 Summer Project Week:RegionalCorticalThicknessTool"
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(New page: {| |thumb|320px|Return to [[2008_Summer_Project_Week|Project Week Main Page ]] |} __NOTOC__ ===Key Investigators=== * UNC: Heather Cody Hazlett, Martin St...) |
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<h1>Approach, Plan</h1> | <h1>Approach, Plan</h1> | ||
| − | Our plan for the project week is to | + | 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) | ||
</div> | </div> | ||
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<h1>Progress</h1> | <h1>Progress</h1> | ||
| + | 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) | ||
</div> | </div> | ||
Latest revision as of 18:56, 30 June 2008
Home < 2008 Summer Project Week:RegionalCorticalThicknessTool Return to Project Week Main Page |
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)
