Automated Cortical Surface Extraction Workflow

Created: 2011-04-06 00:44:05      Last updated: 2011-07-14 00:20:57

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.


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


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LONI Pipeline

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