Freesurfer

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Jonathan Winawer edited this page Jan 31, 2017 · 9 revisions

Freesurfer is an open source software suite for processing and analyzing human brain MRI images: https://surfer.nmr.mgh.harvard.edu/

For a structural MRI scan, Freesurfer can:

perform skull stripping
segment gray matter from white matter
label cortical and subcortical structures

This functionality is a gear on Flywheel.

Freesurfer download and installation

Follow instructions on the [Freesurfer wiki] (https://surfer.nmr.mgh.harvard.edu/fswiki)

Freesurfer integration with vistasoft

FINISH THIS. Test: these Matlab calls should return paths, not empty vectors:
getenv('FREESURFER_HOME')
getenv('FREESURFER_DIR')