Freesurfer

Description

freesurfer website  

Freesurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

Required Modules

Serial

• freesurfer

System Variables

• HPC_{{#uppercase:freesurfer}}_DIR and FREESURFER_HOME - installation directory
• HPC_FREESURFER_BIN - executable directory

Freesurfer configuration variables

The following variables are preset by the freesurfer module:

• SUBJECTS_DIR
• FUNCTIONALS_DIR
• FSFAST_HOME
• MNI_DIR

Matlab configuration

If you do intend to use the functional tools, then add these lines to your ~/matlab/startup.m file:

fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
path(path,fsfasttoolbox);

or load the freesurfer module and run

source $HPC_FREESURFER_DIR/SetUpFreeSurfer.sh

Citation

If you publish research that uses freesurfer you have to cite it as follows:

See [1] in the Freesurfer wiki on how to correctly cite Freesurfer tools.