Freesurfer ​

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

1. Installation ​

1.1. Log into your lab machine and check if Freesurfer is already installed in your software directory:

bash
ls /mnt/work/software

If you see a directory named freesurfer if the software is already installed. If you don't see the directory, continue with the installation:

1.2 Download the Freesurfer package:

bash
# -- principal example (freesurfer v7.2.0)
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'

You might want to check up the lastes release and update the links and numbers in the example above.

1.3 Create a directory and unpack the archive:

bash
# -- make directory
mkdir -p /mnt/work/software/freesurfer

# -- unpack the archive
tar -C /mnt/work/software/ -xzvf /mnt/work/software/freesurfer7.tar.gz

2. Configuration ​

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

bash
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