Neurocontainers

Neurocontainers are individual containerised neuroimaging tools that you can pull and run directly with Docker, Singularity/Apptainer, or distribute over CVMFS. They are the building blocks behind Neurodesktop and the Neurodesk App, and you can also use them on their own in your own pipelines.

Containers are built automatically in the neurocontainers repository and published to Docker Hub, GitHub Container Registry, and as Singularity images on object storage and CVMFS.

Docker Pull and run individual Neurodesk containers with Docker.

Singularity / Apptainer Download and run Singularity/Apptainer containers, including on GPUs.

CVMFS Mount Neurodesk containers from CVMFS for shared HPC and lab systems.

DataLad Use Neurodesk containers with DataLad and ReproNim containerised workflows.

OpenRecon Build Neurocontainers for Siemens OpenRecon scanners.

Windows 11 & WSL Run Neurocontainers on Windows 11 via Windows Subsystem for Linux.

Browse the full catalogue of available containers at neurodesk.org/applications.