Notice

dcm2nii as provided in this build is obsolete! You are encouraged to please use https://github.com/scitran-apps/dcm2niix, which uses modern versions of dcm2niix, and is fully supported and actively maintianed.

scitran/dcm2nii

This Dockerfile will create a MRICRON Docker image that can execute dcm2nii.

Options

Options are set in dcm2nii.ini. Current defaults are set and copied into the container on build.

Optional flags can be passed to the container and will override config in dcm2nii.ini.

Build the Image

To build the image, either download the files from this repo or clone the repo:

./build.sh

Example Usage

To run dcm2nii from this image you can do the following:

docker run --rm -ti \
    -v </path/to/input/data>:/flywheel/v0/input \
    -v </path/to/output>:/flywheel/v0/output \
    scitran/dcm2nii <optional_flags>