wmhchallenge/example repository overview

⁠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