Docker is a container technology, performing operating-system-level virtualisation.
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.
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.def using SPM Standalone and MATLAB Runtime
- singularity.def using GNU Octave
Pre-built images are available from GitHub Packages:
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
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
Check the SPM online documentation.
https://github.com/ReproNim/neurodocker
https://hub.docker.com/r/kaczmarj/neurodocker/
https://github.com/BIDS-Apps/SPM`](https://github.com/BIDS-Apps/SPM)
https://hub.docker.com/r/bids/spm/
https://github.com/mathworks-ref-arch/matlab-dockerfile
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