FSL information

FSL is the FMRIB Software Library. It is a C / C++ / Tcl/Tk package written by the FMRIB in Oxford.

For more information see:

You can find the FSL example data set in /imaging/local/software/fsl/feeds.

The data for the FSL course is in /imaging/local/fsl/fsl_course_data.

Using the latest version of FSL on the CBU cluster

Before using fsl you need to run


This will open a new terminal windonw which will have the latest version of fsl set up and ready to use.

Using a specific version of FSL on the CBU systems

If you need to use a specific version, rather than the one pointed to by /imaging/local/software/fsl/latest, then you can specify which version you need (e.g., version 5.0.7) by running:

cbufsl -v 5.0.7

Alternatively, you can define the path to the version of FSL you want, and put something like this at the end of your ~/.cshrc file:

setenv FSLDIR /imaging/local/software/fsl/v5.0.7/x86_64/fsl
source ${FSLDIR}/etc/fslconf/fsl.csh
set path = (${FSLDIR}/bin $path)

Please note that from version 5.0.10 onwards fslview was deprecated and a new viewer called fsleyes was introduced. fsleyes will not work on the old CBU cluster (login nodes login11 to 20 and login-gpu02 to 05).