Example docker containers for the WMH Segmentation Challenge
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README.md

WMH Segmentation Challenge - MICCAI 2017

Example docker containers for the WMH Segmentation Challenge. These example scripts simply threshold the orig/FLAIR.nii.gz image at 800, but can be used to see how applications can be containerized and run within the challenge.

Python example

A detailed description of the Python example is provided here: http://wmh.isi.uu.nl/methods/example-python/. When this container is run according to the commands below, TEAM-NAME=example:python, YOUR-COMMAND=python /wmhseg_example/example.py, and TEST-ORIG/PRE are the input folders specified here: http://wmh.isi.uu.nl/data/

Matlab example

A detailed description of the matlab example is provided here: http://wmh.isi.uu.nl/methods/example-matlab/. When this container is run according to the commands below, TEAM-NAME=example:matlab, YOUR-COMMAND=wmhseg_example/example, and TEST-ORIG/PRE are the input folders specified here: http://wmh.isi.uu.nl/data/

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.

Docker commands

Containers submitted to the challenge will be run with the following commands:

CONTAINERID=`docker run -dit -v [TEST-ORIG]:/input/orig:ro -v [TEST-PRE]:/input/pre:ro -v /output wmhchallenge/[TEAM-NAME]`
docker exec $CONTAINERID [YOUR-COMMAND]
docker cp $CONTAINERID:/output [RESULT-TEAM]
docker stop $CONTAINERID
docker rm -v $CONTAINERID