Freesurfer Installation

Greydon Gilmore

Download software

Download the .deb file for Freesurfer.

Run the following command (replacing the filename with the one you downloaded):

cd ~/Downloads
sudo dpkg -i freesurfer_ubuntu22-8.1.0_amd64.deb

You will also need to install some dependancies:

sudo apt-get install tcsh
sudo apt-get install libglu1
sudo apt-get install libxss1

Post-Install Configurations

Add Freesurfer to your path:

echo "FREESURFER_HOME=/usr/local/freesurfer" >> ~/.bashrc
echo 'source $FREESURFER_HOME/SetUpFreeSurfer.sh' >> ~/.bashrc

If you have run the install correctly you will see this output when you close and open a new terminal window:

Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME     /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii
SUBJECTS_DIR    /usr/local/freesurfer/subjects
MNI_DIR         /usr/local/freesurfer/mni

Define subjects_dir

FreeSurfer requires an environment variable called SUBJECTS_DIR. This is the directory where subject data is stored, put this in your ~/.bashrc or ~/.zshrc:

export SUBJECTS_DIR=<path to subject data>

Obtain license

You will need to obtain a license key.

Once you obtain the license.txt key file, copy it to your FreeSurfer installation directory. This is also the location defined by the FREESURFER_HOME environment variable.

sudo mv ~/Downloads/license.txt $FREESURFER_HOME
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