fsl - analysis tools for FMRI, MRI and DTI brain imaging
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.
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
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
version to prevent filename conflicts and allow multiple version to
coexist on the same system. For example, the slicer
available as fsl5.0-slicer
. Please note that for using FSL
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.
user interface sometimes refers to an FSLDIR
. On Debian
systems this is /usr/share/fsl/5.0
for FSL version 5.0.
documentation and online help is provided by the fsl-5.0-doc
Questions regarding the usage of FSL
or related theory can be posted on
the FSL mailing list
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
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
The FSL homepage at http://www.fmrib.ox.ac.uk
was written by FMRIB, Oxford, UK.
This manual page was written by Michael Hanke <firstname.lastname@example.org>,
for the Debian project (but may be used by others).