Langue: en

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Version: 334504 (ubuntu - 24/10/10)

Section: 1 (Commandes utilisateur)


fsl - analysis tools for FMRI, MRI and DTI brain imaging


FSL is a comprehensive toolkit for the analysis of medical brain imaging data. It provides tools for data preprocessing, brain extraction, image registration as well as statistical analysis. FSL provides an easy to use GUI.

FSL requires a number of environment variables to be set properly. To achieve this source the config script from /etc/fsl/fsl.sh. One way to do this automatically is to add a line containing

 . /etc/fsl/fsl.sh

to the .bashrc file in a users home directory (or a corresponding file for other shells than bash).

However, it is not necessary to manually source the configuration to use the GUI applications included in FSL.

FSL documentation and online help is provided by the fsl-doc package.

Questions regarding the usage of FSL or related theory can be posted on the FSL mailing list (see http://www.jiscmail.ac.uk/lists/fsl.html).


FSL can be configured to submit jobs to a running Sun Gridengine (SGE). While not all functionality implemented in FSL supports this kind of parallelization, the most demanding processing tools (e.g. POSSUM and FDT) do.

FSL should be able to use SGE even if the SGE_ROOT environment variable is not set, as in the case of the Debian package of SGE. To enable batch processing simply set


in the shell where FSL is running. This can be enabled permanently in


or on a case by case basis.


Main FSL configuration
Default settings for FEAT


fsl-selftest(1), fslview(1)

The FSL homepage at http://www.fmrib.ox.ac.uk


FSL was written by FMRIB, Oxford, UK.

This manual page was written by Michael Hanke <michael.hanke@gmail.com>, for the Debian project (but may be used by others).