FSL

FSL (opens new window) is a comprehensive library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data.

The FSL 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)).

TIP

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

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

Installation using Conda

A simple way if you manage your dependencies with Conda is to install the FSLpy package (opens new window) in your environment:

conda install -c conda-forge fslpy

Installation using flsinstaller

You may install FSL directly on your lab machine. We recoomend that your read up on the official FSL installation (opens new window) documentation if you choose this path.

Requirement

The installation require 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

This is an example of expected output for a successful 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
Downloading...
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
/mnt/work/software/FSL/fsl/fslpython/LICENSE.txt
100%
Stage 2
100%
/tmp/fslpythonYBC3/fslpython_miniconda_installer.log
100%
Post install setup complete
[OK] Post installation setup complete

Configuration

Based on shell setup (opens new window), add the following to your .profile or .bashrc file:

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