PipelineWorkflows_CorticalThickness < CCB

CCB Automated Complete Cortical Thickness Workflow

Pipeline Workflows Home
SIG-FLOW Home
SIG-PNS Home
LONI Pipeline page

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.