A generic generator of Dockerfiles and Singularity recipes

apptainer, containers, docker, dockerfile, linux, neuroscience, nipype, reproducible-research, science, singularity-container
pip install neurodocker==0.8.0



build status docker pulls docker pulls python versions DOI

Neurodocker is a command-line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers.

Please see our website for more information.


Use the Neurodocker Docker image (recommended):

docker run --rm repronim/neurodocker:0.7.0 --help

The Docker images were moved to repronim/neurodocker from kaczmarj/neurodocker.

This project can also be installed with pip:

pip install neurodocker
neurodocker --help

If the pip install command above gives a permissions error, install as a non-root user:

pip install --user neurodocker

Note: it is not yet possible to minimize Docker containers using the Neurodocker Docker image.

Developer installation

Clone the repository and install in editable mode.

git clone
cd neurodocker
python -m pip install --no-cache-dir --editable .[all]

Before committing changes, initialize pre-commit with pre-commit install. This will format code with each commit to keep the style consistent. Neurodocker uses black for formatting.