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/4.1/fsl.sh.   One  way  to   do   this
       automatically is to add a line containing

               . /etc/fsl/4.1/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 fsl#FSLMVERSION-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/4.1 for FSL version 4.1.

       FSL documentation and online help is provided by the fsl-doc-4.1 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/4.1/fsl.sh

       or on a case by case basis.

FILES

       /etc/fsl/4.1/fsl.sh
              Main FSL configuration

       /etc/fsl/4.1/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).