fsl.rst

FSL
===

We are automatically following the FSL 5 release history of `Neurodebian <https://neuro.debian.net>`_.

To use FSL in your jobs, activate it like this:

.. code-block:: bash

   source /etc/fsl/5.0/fsl.sh

Afterwards the :file:`PATH` variable should be set correctly.


FIX
---

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:

.. code-block:: bash

    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