# Freesurfer

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

1. Installation
2. Configuration

# 1. Installation

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

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:

# -- 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:

# -- 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:

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

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