Examples

This page includes examples of using Neurodocker to build containers with popular neuroimaging packages.

Supported software

• _default

• afni

• ants

• bids_validator

• cat12

• convert3d

• dcm2niix

• freesurfer

• fsl

• jq

• matlabmcr

• minc

• miniconda

• mricron

• mrtrix3

• ndfreeze

• neurodebian

• niftyreg

• petpvc

• spm12

• vnc

The commands generate Dockerfiles. To generate Singularity recipes, simply replace

neurodocker generate docker

with

neurodocker generate singularity

To see the options for each package, please run

neurodocker generate docker --help

or

neurodocker generate singularity --help

Note

Neurodocker is meant to create command-line environments. At the moment, graphical user interfaces (like FreeView and FSLEyes) are not installed properly. It is possible that this will change in the future.

FSL

Docker

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:bullseye-slim \
    --fsl version=6.0.7.1 \
> fsl6071.Dockerfile

docker build --tag fsl:6.0.7.1 --file fsl6071.Dockerfile .

This will ask the following question interactively:

FSL is non-free. If you are considering commercial use of FSL, please consult the relevant license(s). Proceed? [y/N]

If you are using neurodocker non-interactively, this problem can be avoided using:

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:buster-slim \
    --yes \
    --fsl version=6.0.4 \
> fsl604.Dockerfile

docker build --tag fsl:6.0.4 --file fsl604.Dockerfile .

# Run fsl's bet program.
docker run --rm -it fsl:6.0.4 bet

AFNI

Docker

neurodocker generate docker \
    --pkg-manager yum \
    --base-image fedora:36 \
    --afni method=binaries version=latest \
> afni-binaries.Dockerfile

docker build --tag afni:latest --file afni-binaries.Dockerfile .

This does not install AFNI’s R packages. To install relevant R things, use the following:

neurodocker generate docker \
    --pkg-manager yum \
    --base-image fedora:36 \
    --afni method=binaries version=latest install_r_pkgs=true \
> afni-binaries-r.Dockerfile

docker build --tag afni:latest-with-r --file afni-binaries-r.Dockerfile .

Todo

Building AFNI from source is currently failing on most tested distributions.

FreeSurfer

Docker

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:bullseye-slim \
    --freesurfer version=7.4.1 \
> freesurfer741.Dockerfile

docker build --tag freesurfer:7.4.1 --file freesurfer741.Dockerfile .

Todo

The minified version on Freesurfer currently fails to build on all tested distributions.

ANTS

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:bullseye-slim \
    --ants version=2.4.3 \
> ants-234.Dockerfile

docker build --tag ants:2.4.3 --file ants-243.Dockerfile .

Note

Building docker images of ANTS from source fails on most tested distributions.

CAT12

CAT12 requires the MCR in the correction version. Miniconda and nipype is optional but recommended to use CAT12 from NiPype.

neurodocker generate docker \
    --base-image ubuntu:22.04 \
    --pkg-manager apt \
    --mcr 2017b \
    --cat12 version=r2166_R2017b \
    --miniconda \
     version=latest \
     conda_install='python=3.11 traits nipype numpy scipy h5py scikit-image' \
> cat12-r2166_R2017b.Dockerfile

docker build --tag cat12:r2166_R2017b --file cat12-r2166_R2017b.Dockerfile .

SPM

neurodocker generate docker \
    --pkg-manager apt \
    --base-image centos:7 \
    --spm12 version=r7771 \
> spm12-r7771.Dockerfile

docker build --tag spm12:r7771 --file spm12-r7771.Dockerfile .

Note

Building docker images of SPM12 from source fails on most tested distributions.

Miniconda

Docker with new conda environment, python packages installed with conda and pip.

neurodocker generate docker \
    --pkg-manager apt \
    --base-image debian:bullseye-slim \
    --miniconda \
        version=latest \
        env_name=env_scipy \
        env_exists=false \
        conda_install=pandas \
        pip_install=scipy \
> conda-env.Dockerfile

docker build --tag conda-env --file conda-env.Dockerfile .

Docker