flavin/dcm2niix repository overview

⁠flavin/dcm2niix

Docker image to execute dcm2niix; built on top of the NeuroDebian docker image⁠.

⁠Build the Image

If you want to build the image yourself, download the source from github⁠.

git clone https://github.com/flavin/dcm2niix-docker
cd dcm2niix-docker
docker build --tag <yourname>/dcm2niix .

⁠Entrypoint

An 'Entrypoint' has been configured for this image at /opt/run, which will do the following:

1. Look for inputs and show help as necessary
2. Run dcm2niix using the inputs provided

⁠Example Usage

To run dcm2niix from this image you can do the following (note that the dcm2niix command is omitted as it is called from the Entrypoint):

docker run -v </path/to/input/data>:/input -v </path/for/output/data>:/output flavin/dcm2niix -z y -f %i_%s -o /output /input

• Note that you are mounting the directory (-v flag) which contains your data in the container at /input and mounting the directory where you want your output data within the container at /output.

• dcm2niix args (relative to the contianer) should be provided at the end of the docker run command, as shown above. Remember that if those inputs are files or other resources, they must also be mounted in the container and the full path to them (again, relative to the container) must be provided.