General Description

FSL (FMRIB Software Library) is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Basic Usage

To make the fsl program available in your current session, use the module command to load the package:

%  module load fsl

Once the package is loaded, the main program can be used by executing the following command:

%  fsl

Advanced Usage

If you need to use fsl to compile and/or use with another program, you may find this script helpful:

%  source $FSLDIR/etc/fslconf/fsl.csh

In addition, the module command provides several environment variables that may be used.

Note Regarding Matlab

If you need to use fsl in conjunction with matlab, you must be sure to use version 8.1 or higher:

%  module load fsl
%  module load matlab/8.1

The fsl tools will then be accessible from within matlab by issuing the system() command. For example,

>> system( 'fslroi' )

Further Information

For more information, see the official FSL website: