FSL is a comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. The suite consists of various command line tools, as well as simple GUIs for its core analysis pipelines. Among others, FSL offers implementations of standard GLM analysis, white matter tractography, tissue segmentation, affine and non-linear co-registration, and independent component analysis (Source: Neurodebian) (opens new window).


Use HTCondor (opens new window) with FSL to speed up analysis by running the tasks in parallel.


Bedpostx (opens new window) also supports GPU, which provides significantly faster results on large datasets.

# Installation using Conda

Simple way for those who manage their dependencies with Conda (opens new window) is to install FSLpy package (opens new window) into their environment using this command:

conda install -c conda-forge fslpy

# Installation using flsinstaller

Our tutorial only briefly summarises the installation, therefore we recommend to read up in official FSL installation (opens new window).


Python 2

git clone https://gist.github.com/cffe4e955249bdde6985d4232a618ab8.git ~/fslinstaller
mkdir -p /mnt/work/software/FSL
mkdir -p /mnt/scratch/tmp
export TMP=/mnt/scratch/tmp/
cd /mnt/work/software/FSL && python ~/fslinstaller/fslinstaller.py
rm -rf ~/fslinstaller
Output log from installation
--- FSL Installer - Version 3.0.15 ---
When asked a question, the default answer is given in square brackets.
Hit the Enter key to accept this default answer.
Where would you like the FSL install to be (including the FSL folder name)? [/usr/local/fsl]: /mnt/work/software/FSL/fsl
Checking FSL package
[OK] File downloaded
Installing FSL software version 6.0.1...
[OK] FSL software installed.
Performing post install tasks
Stage 1
By installing this python distribution you agree to the license terms in
Stage 2
Post install setup complete
[OK] Post installation setup complete

# Configuration

Based on shell setup (opens new window) in .profile or .bashrc add following:

export FSLDIR=/mnt/work/software/fsl
source "${FSLDIR}/etc/fslconf/fsl.sh"