Example docker containers for the IVD Segmentation Challenge. These example scripts simply threshold the /fat.nii.gz image at 20, but can be used to see how applications can be containerized and run within the challenge.
A detailed description of the Python example is provided here: https://ivdm3seg.weebly.com/methods.html.
In order to run matlab scripts in a container, the script has to be compiled with the matlab compiler. Within the container, we install the corresponding matlab runtime to execute the compiled script.
Containers submitted to the challenge will be run with the following commands:
CONTAINERID=`docker run -dit -v [TEST-DIR]:/input:ro -v /output ivdm3seg/[TEAM-NAME]`
docker exec $CONTAINERID [YOUR-COMMAND]
docker cp $CONTAINERID:/output [RESULT-TEAM]
docker stop $CONTAINERID
docker rm -v $CONTAINERID