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 ICVMapp3r¶
If you want to use Docker to run ICVMapp3r, you must first install Docker on your system. While the installation method differs per system, instructions can be found for the following:
Once Docker is installed, open the docker terminal and test it with the command
docker run hello-world
Pulling ICVMapp3r’s Docker immge¶
While you can download various Docker images, for the sake of this tutorial pull the ICVMpp3r image
docker pull mgoubran/icvmapper:latest
Verify that the image was pulled successfully by checking all images on your system
Running the Docker image¶
If you have installed Docker for the first time. and have verified that the
hello-world image was running, then ICVMapper can be run on your syste.
The simplest way to run the container is:
docker run -it mgoubran/icvmapper seg_icv -t1 /ICVMapp3r/data/test_case/mprage.nii.gz
Using ICVMapper 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 ICVMapper is stored as a Docker image, it can be built in singularity by calling:
singularity build icvmapper.sif docker://mgoubran/icvmapper
To ensure that the Docker image has been built in Singularity, run
singularity exec icvmapper.sif icvmapper --help