FreeSurfer 2016

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FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer is the structural MRI analysis software of choice for the Human Connectome Project. 1

Installed version

The currently installed version is provided... on environment hpc-env/6.4:


on environment hpc-env/8.3:


Using FreeSurfer

If you want to find out more about FreeSurfer on the HPC Cluster, you can use the command

module spider FreeSurfer

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load hpc-env/8.3
module load  FreeSurfer

Always remember: this command is case sensitive!

Testing FreeSurfer

If you load FreeSurfer for the first time, the folders freesurfer/subjects will be created in your home directory. If you want to try out the program, you can use the sample files stored in the installation directory. Copy the samples into your personal folder:

cp -r $EBROOTFREESURFER/subjects/sample* ~/freesurfer/subjects
cd ~/freesurfer/subjects

Now you have stored two sample files to work with in your subjects directory. An example usage of these files, to create a new subject, called 'ernie', and to run the first stage (averaging, intensity normalization and skull-strip) would be:

recon-all -s ernie -i $SUBJECTS_DIR/sample-001.mgz -i $SUBJECTS_DIR/sample-002.mgz -autorecon1


The full documentation can be found here.