Freesurfer

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

To check if Freesurfer was downloaded successfully, open Matlab and type the following in the command window:
getenv('FREESURFER_HOME')
getenv('SUBJECTS_DIR')

These Matlab calls should return paths, not empty vectors:
/Applications/freesurfer
Your/Freesurfer_subjects/directory/Freesurfer_subjects

Tip: It might be tedious to add Freesurfer to your path every time you open up Matlab.