SPM Containers

This repository provides github action workflows for automatic docker and singularity image creation. They are triggered by releasing a new SPM version.

Containers

The containers are hosted on the GitHub Container Registry

docker pull ghcr.io/spm/spm-docker:docker-matlab
docker pull ghcr.io/spm/spm-docker:docker-octave

singularity pull oras://ghcr.io/spm/spm-docker:singularity-matlab
singularity pull oras://ghcr.io/spm/spm-docker:singularity-octave

Usage

For example, to start SPM with its graphical user interface, use the following:

xhost +local:docker  
docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp:/tmp -v /tmp/.X11-unix:/tmp/.X11-unix ghcr.io/spm/spm-docker:docker-matlab fmri

If the container's root filesystem is mounted as read only (--read-only flag), you need to bind mount an extra volume:

-v /tmp/.matlab:/root/.matlab

Technology

Docker

Docker is a container technology, performing operating-system-level virtualisation.

Singularity

Singularity is another container technology that performs operating-system-level virtualization. One of the main uses of Singularity is to bring containers and reproducibility to scientific computing and HPC.

• SingularityCE
• Apptainer

SPM Containers Creation

The official SPM Dockerfiles:

• Dockerfile using the SPM Standalone
• Dockerfile using GNU Octave
• Dockerfile using the SPM Standalone and selected third-party toolboxes (outdated)

The singularity sif images are created from the docker images.

Documentation

Check the SPM online documentation.

See also

Neurodesk

https://www.neurodesk.org/

Neurodocker

https://github.com/ReproNim/neurodocker
https://hub.docker.com/r/kaczmarj/neurodocker/

SPM BIDS-App

https://github.com/BIDS-Apps/SPM`](https://github.com/BIDS-Apps/SPM)
https://hub.docker.com/r/bids/spm/

MATLAB Dockerfile

https://github.com/mathworks-ref-arch/matlab-dockerfile

Singularity

SingularityCE User Guide

sudo singularity build spm12.sif spm12-octave.def
singularity exec spm12.sif
./spm12.sif --help

(how to install singularity on Ubuntu)

Docker Hub (deprecated)

SPM Docker images used to be hosted on Docker Hub but this is now deprecated and the GitHub Packages Container Registry should be used instead.

docker pull spmcentral/spm:latest
docker pull spmcentral/spm:octave