Neurodocker is a command-line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers.
Examples:
- Canonical examples
- Assorted examples
- Minimize existing Docker image
- Example of minimizing Docker image for FreeSurfer recon-all
Use the Neurodocker Docker image (recommended):
$ docker run --rm kaczmarj/neurodocker:0.4.0rc1 --helpThis project can also be installed with pip:
$ pip install neurodocker
$ neurodocker --helpIf the pip install command above gives a permissions error, install as a non-root user:
$ pip install --user neurodockerNote: it is not yet possible to minimize Docker containers using the Neurodocker Docker image.
| software | argument | description |
|---|---|---|
| AFNI | version* | latest |
| method | binaries (default), source. Install pre-compiled binaries or build form source. | |
| install_path | Installation path. Default /opt/afni-{version}. |
|
| install_r | If true, install R. | |
| install_r_pkgs | If true, install R and AFNI's R packages. | |
| install_python2 | If true, install Python 2. | |
| install_python3 | If true, install Python 3. | |
| ANTs | version* | 2.2.0, 2.1.0, 2.0.3, or 2.0.0. If method=source, version can be a git commit hash or branch. |
| method | binaries (default), source. | |
| install_path | Installation path. Default /opt/ants-{version}. |
|
| cmake_opts | If method=source, options for cmake. |
|
| make_opts | If method=source, options for make. |
|
| Convert3D | version* | 1.0.0 or nightly. |
| method | binaries (default) | |
| install_path | Installation path. Default /opt/convert3d-{version}. |
|
| dcm2niix | version* | latest, git commit hash or branch. |
| method | source (default) | |
| install_path | Installation path. Default /opt/dcm2niix-{version}. |
|
| cmake_opts | If method=source, options for cmake. |
|
| make_opts | If method=source, options for make. |
|
| FreeSurfer | version* | 6.0.0-min |
| method | binaries (default) | |
| install_path | Installation path. Default /opt/freesurfer-{version}. |
|
| exclude_paths | Sequence of path(s) to exclude when inflating the tarball. | |
| license_path | Relative path to license file. If provided, this file will be copied into the Docker image. Must be within the build context. | |
| FSL** | version* | 5.0.11, 5.0.10, 5.0.9, 5.0.8 |
| method | binaries (default) | |
| install_path | Installation path. Default /opt/fsl-{version}. |
|
| Matlab Compiler Runtime | version* | 2018a, 2012-17[a-b], 2010a |
| method | binaries (default) | |
| install_path | Installation path. Default /opt/matlabmcr-{version}. |
|
| MINC | version* | 1.9.15 |
| method | binaries (default) | |
| install_path | Installation path. Default /opt/minc-{version}. |
|
| Miniconda | version | latest (default), all other hosted versions. |
| install_path | Installation path. Default /opt/miniconda-{version}. |
|
| env_name* | Name of this conda environment. | |
| conda_install | Packages to install with conda. E.g., conda_install="python=3.6 numpy traits" |
|
| pip_install | Packages to install with pip. |
|
| activate | If true (default), activate this environment in container entrypoint. | |
| MRtrix3 | version* | 3.0 |
| method | binaries (default) | |
| install_path | Installation path. Default /opt/mrtrix3-{version}. |
|
| NeuroDebian | os_codename* | Codename of the operating system (e.g., stretch, zesty). |
| server* | Server to download NeuroDebian packages from. Choose the one closest to you. See neurodocker generate docker --help for the full list of servers. |
|
| full | If true (default), use non-free sources. If false, use libre sources. | |
| PETPVC | version* | 1.2.2, 1.2.1, 1.2.0-b, 1.2.0-a, 1.1.0, 1.0.0 |
| method | binaries (default) | |
| install_path | Installation path. Default /opt/petpvc-{version}. |
|
| SPM12 | version* | r7219, r6914, r6685, r6472, r6225 |
| install_path | Installation path. Default /opt/spm12-{version}. |
|
| Note: Matlab Compiler Runtime is installed when SPM12 is installed. |
* required argument.
** FSL is non-free. If you are considering commercial use of FSL, please consult the relevant license.
Please see the examples directory.
The canonical examples install ANTs version 2.2.0 on Ubuntu 18.04.
$ docker run --rm kaczmarj/neurodocker:0.4.0rc1 generate docker \
--base ubuntu:18.04 --pkg-manager apt --ants version=2.2.0
# Build image by piping Dockerfile to `docker build`
$ docker run --rm kaczmarj/neurodocker:0.4.0rc1 generate docker \
--base ubuntu:18.04 --pkg-manager apt --ants version=2.2.0 | docker build -Install ANTs on Ubuntu 18.04.
$ docker run --rm kaczmarj/neurodocker:0.4.0rc1 generate singularity \
--base ubuntu:18.04 --pkg-manager apt --ants version=2.2.0Neurodocker must be pip installed for container minimization.
In the following example, a Docker image is built with ANTs version 2.2.0 and a functional scan. The image is minified for running antsMotionCorr. The original ANTs Docker image is 1.85 GB, and the "minified" image is 365 MB.
# Create a Docker image with ANTs, and download a functional scan.
$ download_cmd="curl -sSL -o /home/func.nii.gz http://psydata.ovgu.de/studyforrest/phase2/sub-01/ses-movie/func/sub-01_ses-movie_task-movie_run-1_bold.nii.gz"
$ neurodocker generate docker -b centos:7 -p yum --ants version=2.2.0 --run="$download_cmd" | docker build -t ants:2.2.0 -
# Run the container.
$ docker run --rm -itd --name ants-reprozip-container --security-opt=seccomp:unconfined ants:2.2.0
# Output a ReproZip pack file in ~/neurodocker-reprozip-output with the files
# necessary to run antsMotionCorr.
# See https://github.com/stnava/ANTs/blob/master/Scripts/antsMotionCorrExample
$ cmd="antsMotionCorr -d 3 -a /home/func.nii.gz -o /home/func_avg.nii.gz"
$ neurodocker reprozip-trace ants-reprozip-container "$cmd"
# Create a Docker container with the contents of ReproZip's trace.
$ reprounzip docker setup neurodocker-reprozip.rpz test