06-06-02 Graham Wideman
|FreeSurfer Process Diagram
Article created: 2003-03-10
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.
A diagrammatic overview of the main FreeSurfer process, proceeding generally
from top to bottom.
- Cube shapes: volume of voxels (or equivalently a stack of 2-D images).
- Shapes with axis arrows: Surface files.
- 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
- 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
or back to Understanding FreeSurfer