FreeSurfer

Set-up

Load the FreeSurfer module with  module load freesurfer. This will load the default version. Then, to continue configuring your environment, you must source the setup script for Freesurfer. Do this with the following command that corresponds to the Linux shell you are using. If using bash, use:

source $FREESURFER_HOME/SetUpFreeSurfer.sh

If using tcsh, use:

source $FREESURFER_HOME/SetUpFreeSurfer.csh

To finish configuring FreeSurfer, set the the FreeSurfer environment variable SUBJECTS_DIR to the directory of your subject data. The SUBJECTS_DIR variable defaults to the FREESURFER_HOME/subjects directory, so if this is your intended directory to use the enviornment set-up is complete.

To alter the SUBJECTS_DIR variable, however, again use the following command that corresponds to the Linux shell you are using. For bash:

export SUBJECTS_DIR=<path to subject data>

For tcsh:

setenv SUBJECTS_DIR=<path to subject data>

Note that you can set the SUBJECT_DIR variable before or after sourcing the setup script.

The cuda applications from FreeSurfer requires CUDA 5 library (which is not avaiable through module system). To set up cuda environment, run the following command after load the FreeSurfer module. If  you are using bash, run:

source $FREESURFER_HOME/bin/cuda5_setup.sh

If using tcsh, use:

source $FREESURFER_HOME/bin/cuda5_setup.csh