Docker / Singularity

If you intend to use Singularity, scroll down to the Singularity section. Otherwise, the steps to use the image in Docker can be found below.

Before using Docker image for HippMapp3r

If you want to use Docker to run HippMapp3r, you must first install Docker on your system. While the installation method differs per system, instructions can be found for the following:

• Ubuntu

• Windows

• Mac

Once Docker is installed, open the docker terminal and test it with the command

docker run hello-world

Pulling HippMapp3r’s Docker immge

While you can download various Docker images, for the sake of this tutorial pull the HippMpp3r image

docker pull mgoubran/hippmapper:latest

Verify that the image was pulled successfully by checking all images on your system

docker images

Running the Docker image

If you have installed Docker for the first time. and have verified that the hello-world image was running, then HippMapper can be run on your syste.

The simplest way to run the container is:

docker run -it mgoubran/hippmapper seg_hipp -t1 /hippMapp3r/data/test_case/mprage.nii.gz

To run the Docker container in an interactive shell, run

docker run --rm -v {enter/path/here}:/root -it --entrypoint /bin/bash mgoubran/hippmapper

Using HippMapper on Singularity

Docker images can still be used on Singularity. This is especially good if you are processing images using Compute Canada clusters. The following instructions are based on the steps provided on the Compute Canada wiki.

Load the specific Singularity module you would like to use.

module load singularity/3.5

Although HippMapper is stored as a Docker image, it can be built in singularity by calling:

singularity build hippmapper.sif docker://mgoubran/hippmapper

To ensure that the Docker image has been built in Singularity, run

singularity exec hippmapper.sif hippmapper --help