About

This is a very unofficial repo for FSL singularity recipes used at the MPIB. A while ago we used to automatically push images to the amazing singularity hub. Since that project has been abandoned, we use this repo primarily as a recipe reference.

The base container is Debian 10 and it should work fine with CUDA as well. For very old installations we keep some cuda-8 recipes around, but they are not necessary to run a current release of FSL.

Build an image

git clone https://github.com/MPIB/singularity-fsl
cd singularity-fsl
export VERSION=6.0.6.1
sudo singularity build fsl-$VERSION.sif Singularity.$VERSION

Run in image

singularity exec fsl-$VERSION.sif fslmaths
singularity exec --nv fsl-$VERSION eddy_cuda9.1

older, pre-built images from singularity-hub

Some older images are still available on the read-only mirror provided by datalad.org and can be pulled directly.

(last updated in April 2021)

# Download a (versioned) container
singularity pull shub://MPIB/singularity-fsl:6.0.3

FSL

Project Home: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/

These are containers primarily used at the MPI for Human Development.

Cuda

Starting with Singularity 6.0.2 we include Nvidia CUDA through Debian backports repositories. Make sure your Nvidia driver on the host supports it and add the --nv flag with singularity.

Note

Please be aware of FSL's strict license regarding non-commercial use.