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We are automatically following the FSL 5 release history of `Neurodebian <http://neuro.debian.net>`_.
To use FSL in your jobs, activate it like this:
Afterwards the :file:`PATH` variable should be set correctly.
We have set up a running version of `FSL Fix <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX>`_.
Currently it is not using FSL's internal qsub so it only makes sense to
parallelize over a number of subjects. Example:
for icadir in *ica ; do
echo "module load fsl_fix" >> tmpjob
echo "source /etc/fsl/5.0/fsl.sh" >> tmpjob
echo "fix ${icadir} /opt/software/fix/1.06/training_files/Standard.RData 20" >> tmpjob
qsub -N fix_foobar -j oe -d. tmpjob
rm -f tmjob
done