SPM Containers

Technology

Docker

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

• Docker

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

Official SPM Dockerfile and singularity.def (using the SPM Standalone or GNU Octave):

Dockerfile for SPM

• Dockerfile using SPM Standalone and MATLAB Runtime
• Dockerfile using GNU Octave

Singularity Definition File for SPM

• singularity.def using SPM Standalone and MATLAB Runtime
• singularity.def using GNU Octave

Container Registry

Pre-built images are available from GitHub Packages:

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

See also a Docker image for SPM Standalone and selected third-party toolboxes with the MATLAB Runtime:

docker pull ghcr.io/spm/spm-docker:docker-tbx

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

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