Automated Cortical Surface Extraction Workflow

This workflow takes raw un-skull-stripped volumes and generates a cortical surface model using <font>FreeSurfer</font>^? and CCB tools.

Problem addressed by this workflow

There are many ways to generate cortical surface models based on MRI data. Here is one of them. Eventually, there will be a new Learning-based Cortical Surface Modeling Pipeline, as well.

• Input is Raw MRI T1-weighted volume
• CCB/FreeSurfer Cortical Surface extractor that the SIG-Shape team developed and we validated in 2009.
• Results should be stored in OBJ/DFS or other ShapeTools understandable formats.

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

URL: http://www.loni.ucla.edu/twiki/bin/view/CCB/PipelineWorkflows_CorticalSurfaceExtraction

Try this workflow now online!