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CCB Automated Complete Cortical Thickness Workflow
Overview - Cortical Thickness Workflow
This workflow takes raw un-skull-stripped volumes and generates the Left and Right cortical surfaces. It also estimates the cortical thickness at each vertex on the cortical surfaces and maps these GM-thickness values on each vertex. The results may be viewed using ShapeViewer.
Problem addressed by this workflow
Identifying local Gray-Matter cortical thickness at each location on the left and right cortices. The resulting thickness maps are available in text/ASCII format as well as as color-attributes anchored on each vertex of hte triangulated cortical surfaces and can be displayed using text-file viewers/editors or ShapeViewer.
Detailed Workflow Usage & Specifications
- Input: Any volumetric file format can be used for the raw unskull-stripped input images (e.g., DICOM, Directories, Analyze, MNC, Nifti, etc.)
- Auto Surface extraction
- FreeSurfer's reconall is used to generate the first estimate of the L/R cortical surfaces
- SIG-SHAPE's cortical surface processing (topological correction) is applied on the surfaces
- Tissue Label Processing
- ImageVoxelMapIntensity Mapper - relabels the tissue classified (WM, GM, CSF, Background) intensities into a standard schema (e.g., /ifs/ccb/CCB_SW_Tools/others/ShapeVolumeTools/CorticalThickness/lib/maps/brainsuite_pvc.map):
- Map 3 1
- Map 4 2
- Map 5 0
- Map 6 Max 255
- File renaming module (necessary because of a bug in ImageVoxelMapIntensity Mapper, which outputs files with these names *.img.img and *.img.hdr, instead of *.img and *.hdr)
- Convert the Analyze volume to MNC - we need to know the origin of hte coordinate system to be able to accurately co-register the volumetric data and the reconstructed cortical surfaces)
- Cortical Thickness: This module computes the cortical thickness of a CSF/GM/WM segmented image and returns the thickness measurements at the vertices of a mesh provided by the user. This is implemented using AIR's distance_quick and gsmooth and ShapeTools' ShapeTransform, ShapeAttribute and ImageToShapeAttribute.
Pipeline Workflows
Footnotes
- Outputs and results: ASCII/Text thickness values (one line per vertex) or color-coded (attributes) on DX surface files.
- Expected times: about 24 hrs.
- Limitations: For some data/populations, the pre-processing steps (skull-stripping, tissue segmentation, etc.) may need to be improved/replaced by analogous processes (e.g., SSMA for Skull-stripping).
- Contact person/group: SIG-SHAPE Team
- Pubs: Publications
- Grants: U54 RR021813, P41 RR013642
- Tools/packages used in this workflow: FSL, FreeSurfer, CCB tools.
- Notes: Under validation (11/05/09)
| META FILEATTACHMENT | Automated_CorticalThickness_Fig1.png | attr="h" comment="" date="1257445775" path="Automated_CorticalThickness_Fig1.png" size="339860" user="dinov" version="1.1" |
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| META FILEATTACHMENT | Automated_CorticalThickness_Fig2.png | attr="h" comment="" date="1257445821" path="Automated_CorticalThickness_Fig2.png" size="998724" user="dinov" version="1.1" |
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| META FILEATTACHMENT | CCB_CorticalSurfaceExtraction_GM_Thickness_2009.pipe | attr="h" comment="" date="1257445835" path="CCB_CorticalSurfaceExtraction_GM_Thickness_2009.pipe" size="165451" user="dinov" version="1.1" |
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