Skip to content

FSL

Library of analysis tools for FMRI, MRI and diffusion brain imaging data

Homepage Version(s): 6.0.5

FSL requires an environment module

In order to use FSL, you must first load the appropriate environment module: 

module load fsl

FSL (FMRIB Software Library) is a comprehensive suite of analysis tools developed by the Oxford Centre for Functional MRI of the Brain (FMRIB). It is widely used in neuroimaging research for the analysis of functional MRI (fMRI), structural MRI, and diffusion-weighted imaging (DWI/DTI) data.

FSL provides both command-line tools and graphical user interfaces (GUIs), allowing users to build reproducible analysis pipelines while still supporting interactive exploration and visualization.

Using FSL on RCC Resources#

Before running any FSL commands, you must load the FSL module and initialize the environment.

1
2
$ module load fsl
$ source $FSLDIR/etc/fslconf/fsl.sh

After sourcing the setup script, all standard FSL commands will be available in your shell.

You can verify the installation with: 

1
$ flirt -version

Launching FSL GUI#

In order to use the FSL graphical user interface (GUI) applications, you will need to use the RCC Desktop on Open OnDemand (OOD) or a graphical SSH connection to RCC resources. Once this is established, you can launch FSL GUI applications by running the following command in your terminal:

1
$ fsleyes

Example: Running feat for fMRI Analysis#

FEAT (FMRI Expert Analysis Tool) is one of the core components of FSL and provides a complete pipeline for fMRI preprocessing, statistical modeling, and group analysis.

Once a design file has been created, FEAT can be run non-interactively: 

1
$ feat design.fsf
This will launch the full FEAT pipeline using the parameters defined in the file. FEAT creates an output directory ending in .feat containing all results.