FSL is a comprehensive library of analysis tools for FMRI, MRI, and DTI brain imaging data. It runs on both Linux (e.g. Apple machines) and Windows operating systems, and requires a Virtual Machine for Windows. Most of the FSL tools can be run from both the command line and as GUIs ("point-and-click" graphical user interfaces).

Using FSL on RCC Resources

To use FSL, set up the environment variables (i.e., add to your .bashrc file) using the following commands:

## FOR BOTH VERSIONS (DO THIS FIRST)
$ module load gnu python/2

## FOR VERSION 6.0.5
$ export FSLDIR=/gpfs/research/software/FSL/6.0.5_source/fsl
$ . ${FSLDIR}/etc/fslconf/fsl.sh
$ export PATH=$PATH:/gpfs/research/software/FSL/6.0.5_source/fsl/bin
$ fsl_sub_config shell

## FOR VERSION 6.0.2
$ export FSLDIR=/gpfs/research/software/FSL/6.0.2/install
$ export PATH=$PATH:/gpfs/research/software/FSL/6.0.2/install/bin

For more information on FSL, refer to the official website.