Last edit: 06-06-02 Graham Wideman

FreeSurfer

2006-06-01: Note that this page pertains to the "Freesurfer 2001 stable" version. The subsequent 2006 stable version has added a number of advancements, including:
-- improved level of success of the automated steps, reducing manual interventions
-- subcortical region segmentation as a separate branch
-- labeling of cortical surface regions at the end
... however the main surface-finding strategy sketched here is the same.

Overview

A diagrammatic overview of the main FreeSurfer process, proceeding generally from top to bottom.

Key:

• Cube shapes: volume of voxels (or equivalently a stack of 2-D images).
• Shapes with axis arrows: Surface files.

Notes:

• Bert Images: All the images above are real images from the sample Bert data from the FreeSurfer website. To see the samples in more detail, visit this page.  (Exception: the flattened surface -- this is copied from one of the Dale, Fischl, Sereno papers).
   
• Input Data and Resampling: FreeSurfer currently accepts input data in a number of formats. The initial steps align, motion-correct, average the data. Along the way the data is resampled to 256^3 1 mm voxels
   
• Make Final Surfaces uses a number of files from previous steps. These are not shown with explicit arrows, but instead with asterisks.
   
• Inflate to Sphere, Register and Flatten are all optional steps

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