Freesurfer

Freesurfer (opens new window) is an open source software suite for processing and analyzing (human) brain MRI images.

Installation

Check if Freesurfer is already installed in software directory:

ls /mnt/work/software

If not installed, download the Freesurfer package:

wget -O /mnt/work/software/freesurfer7.tar.gz 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.2.0/freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz'

Then, create a directory and unpack the archive:

mkdir -p /mnt/work/software/freesurfer
tar -C /mnt/work/software/ -xzvf /mnt/work/software/freesurfer7.tar.gz

Configuration

Add the following lines to your ~/.bashrc config to be able to run freesurfer tools:

PATH="$PATH:/mnt/work/software/freesurfer/bin"

export FREESURFER_HOME=/mnt/work/software/freesurfer
export FSFAST_HOME=/mnt/work/software/freesurfer/fsfast
export FSF_OUTPUT_FORMAT=nii
export SUBJECTS_DIR=/mnt/work/software/freesurfer/subjects
export MNI_DIR=/mnt/work/software/freesurfer/mni