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FSL

FMRIB Software Library

Homepage Version(s): 6.0.5, 6.0.2

FSL requires an environment module

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

module load gnu python/2

FSL is a comprehensive library of analysis tools for FMRI, MRI, and DTI brain imaging data.

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 using the following commands:

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## 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