Singularity image definition for FSL

Making it easier to start using FSL on e.g. HPC.

License

See LICENSE.txt, particularly the conditions regarding commercial use.

Running FSL within a Singularity container using this Singularity image definition

The quickest way to start using FSL via this Singularity image is to pull the image from the SingularityHub on-line repository:

export SINGULARITY_CACHEDIR="/home/$USER/singularity_cache"
mkdir -p "${SINGULARITY_CACHEDIR}"
singularity pull --name fsl-debian-stretch-singularity-latest.sif shub://rses-singularity/fsl-debian-stretch-singularity:latest 
singularity exec "${SINGULARITY_CACHEDIR}/fsl-debian-stretch-singularity-latest.sif" /bin/bash

After running singularity exec you are then able to run commands 'within' a FSL 'container' e.g. fsl-selftest or fsl5.0-gps. Note that most FSL commands start with fsl5.0-.

A note re SingularityHub: the FSL image provided via SingularityHub is rebuilt whenever there is a push to this GitHub repository.

Building a Singularity image and running a FSL container without using SingularityHub

If you don't want to use the SingularityHub-built image then you can build it yourself on your own machine (not HPC):

1. Make sure you have Singularity installed.
2. Ensure you're read the FSL license.
3. Inspect the Singularity image definition in this repo; this includes steps to:
   • Install FSL.
   • Install the FSL Evaluation and Example Data Suite (FEEDS).
4. Start building an image file:

   sudo SINGULARITY_TMPDIR=$HOME/.cache/singularity singularity build ./fsl-debian-stretch-singularity.sif ./Singularity

To start a FSL container using this image:

singularity exec ./fsl-debian-stretch-singularity.sif /bin/bash

then from the resulting shell start the FSL command you want to use.

Testing FSL inside a container

Run:

fsl-selftest