Difference between revisions of "DBP2:UNC:Local Cortical Thickness Pipeline"
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:* Cortical surface inflation: module in progress | :* Cortical surface inflation: module in progress | ||
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=== Future work === | === Future work === |
Revision as of 00:31, 14 December 2008
Home < DBP2:UNC:Local Cortical Thickness PipelineBack 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.
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)
- 2.1 T1-weighted atlas deformable registration
- 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
- Iterative smoothing using relaxation operator (considering average vertex) and L2 norm of the mean curvature as a stopping criterion
- 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
- 1. Tissue segmentation
Download
Usage
Command line execution
Step by step command line execution
Pipeline validation
Analysis on a small pediatric dataset
Tests will be computed on a small pediatric dataset which includes 2 year-old and 4 year-old cases.
- 16 autistic cases
- 1 developmental delay
- 3 normal control
Comparison to state of the art
We would like to compare our pipeline with FreeSurfer. We will thus perform a regional statistical analysis using Pearson's correlation coefficient on a pediatric dataset including 90 cases.
Two distinct groups are considered: 2 year-old cases and 4 year-old cases.
Planning
In progress
- Cortical surface inflation: module in progress
- Mesh needs to be fixed at some location to have a correct inflation
Future work
- UNC Slicer3 external modules available on NITRIC
- Workflow for individual analysis (Slicer3 external module using BatchMake)
- Workflow for group analysis