.. _`fsl6-dockerimage`:

==================
fsl6 Docker Image
==================

.. contents::
   :depth: 1
   :local:

.. admonition:: Compute Resources

    - Have questions or need help with compute, including activation or issues? Follow `this link. <https://washu.atlassian.net/servicedesk/customer/portal/2/group/6/create/43>`__
    - :ref:`User Agreement <compute-user-agreement>`

.. admonition:: Docker Usage

    - The information contained on this page assumes that you have a knowledge base of using Docker to create images and push them to a repository for use. If you need to review that information, please see the links below.
    - :ref:`Docker and the RIS Compute Service <docker-on-compute>`
    - :ref:`Docker Basics: Building, Tagging, & Pushing A Custom Docker Image <ris-docker-basics>`


.. _`fsl6-dockerimage-software`:

Software Included
-----------------

- Functional MRI: FEAT, MELODIC, FABBER, BASIL, VERBENA
- Structural MRI: BET, FAST, FIRST, FLIRT & FNIRT, FSLVBM, SIENA & SIENAX, MIST, BIANCA, MSM, fsl_anat
- Diffusion MRI: FDT, TBSS, XTRACT, eddy, topup, eddyqc
- GLM /Stats: GLM general advice, Randomise, PALM, Cluster, FDR, Dual Regression, Mm, FLOBS
- Other: FSLeyes, FSLView, Fslutils, Atlases, Atlasquery, SUSAN, FUGUE, MCFLIRT, Miscvis, POSSUM, BayCEST


.. _`fsl6-dockerimage-dockerfile`:

Dockerfile
----------

Versions
~~~~~~~~

- Docker image hosted at

    .. code::

        gcr.io/ris-registry-shared/fsl6

- Minimum Docker image hosted at

    .. code::

        gcr.io/ris-registry-shared/fsl6_min

- Code repository is located at `BitBucket <https://bitbucket.wustl.edu/projects/RISDEV/repos/bayly-fsl/browse>`_
  and requires Wustl VPN connection and a wustlkey to access.


.. _`fsl6-dockerimage-run`:

Run on LSF
----------

Preserve Environment variables
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

- Paths inside the container are not being preserved unless one sets this variable for the whole session.
    - `export LSF_DOCKER_PRESERVE_ENVIRONMENT=false`
    - Prepend `LSF_DOCKER_PRESERVE_ENVIRONMENT=false` before an individual bsub command (in which case the variable is only false for that command).
- If one fails to set preserve environment variable to false, one would have to provide each application's full path.

`bsub` Command
~~~~~~~~~~~~~~

.. note::

    If you are a member of more than one compute group, you will be prompted to specify an LSF User Group with ``-G group_name`` or by setting the ``LSB_SUB_USER_GROUP`` variable.

- Interactive Session

    .. code::

        bsub -Is -q general-interactive -a 'docker(gcr.io/ris-registry-shared/<VERSION>)' /bin/bash

- Alternatively, if you want the preserve environment to only be false for one command.

    .. code::

        LSF_DOCKER_PRESERVE_ENVIRONMENT=false bsub -Is -q general-interactive -a 'docker(gcr.io/ris-registry-shared/<VERSION>)' /bin/bash

- Non-Interactive

    .. code::

        bsub -a 'docker(gcr.io/ris-registry-shared/<VERSION>)' {command & arguments to run}