neurodocker 0.4.0rc1

Create custom containers for neuroimaging

Neurodocker

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

Examples:

• Canonical examples
  • Docker
  • Singularity
• Assorted examples
• Minimize existing Docker image
• Example of minimizing Docker image for FreeSurfer recon-all

Installation

Use the Neurodocker Docker image (recommended):

$ docker run --rm kaczmarj/neurodocker:0.4.0rc1 --help

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.

Supported software

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.

Examples

Please see the examples directory.

Canonical examples

The canonical examples install ANTs version 2.2.0 on Ubuntu 18.04.

Docker

$ 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 -

Singularity

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=2.2.0

Minimize existing Docker image

Neurodocker 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