NAME

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

DESCRIPTION

       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  a  broad  spectrum  of  statistical
       analyses.  FSL provides an easy to use GUI.

       FSL  requires  a  number of environment variables to be set properly.  To achieve this, please source the
       config script from /etc/fsl/5.0/fsl.sh.  One way to do this automatically is to add a line containing

               . /etc/fsl/5.0/fsl.sh

       to the .bashrc file in a users home directory (or a corresponding file for other shells than  bash).  You
       may need to create such a file first.

       Alternatively,  the  Debian  package  installs  symlinks  for all FSL tools in /usr/bin that take care of
       loading  the  appropriate  configuration  automatically.   The  symlink  names  are  prefixed  with   the
       corresponding FSL version to prevent filename conflicts and allow multiple version to coexist on the same
       system.  For  example,  the  slicer command is available as fsl5.0-slicer. Please note that for using FSL
       tools via these symlinks it is not necessary to perform the setup procedure describe above. However, this
       convenience feature is Debian-specific. Scripts that employ FSL commands and are intended  to  be  shared
       with others should rely on unprefixed command names and the FSL environment variable setup.

       The  FSL  user  interface sometimes refers to an FSLDIR. On Debian systems this is /usr/share/fsl/5.0 for
       FSL version 5.0.

       FSL documentation and online help is provided by the fsl-5.0-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).

PARALLELIZATION

       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

              FSLPARALLEL=1

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

              /etc/fsl/5.0/fsl.sh

       or on a case by case basis.

FILES

       /etc/fsl/5.0/fsl.sh
              Main FSL configuration

       /etc/fsl/5.0/feat.tcl
              Default settings for FEAT

SEE ALSO

       fsl-selftest(1), fslview(1)

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

AUTHOR

       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).

Michael Hanke                                    September 2012                                       FSL-5.0(1)