To build the docker image cd to the docker folder. In this folder run
docker build -t elastixdocker:v0 .
To build the docker image. The image is based on a ubuntu 18.04 based image and uses elastix version 5.0.0.
To run docker container run the following command
docker run -it -v path/to/ElastixExperimentTracker:/home/appuser/elastix elastixdocker:v0
where path/to/ElastixExperimentTracker is the absolute path to this cloned github repository. The -v flag in docker binds a volume from the host machine to the docker container. In this case we make it so that the docker can acsess the ElastixExperimentTracker on the host machine by binding it to a folder on in the docker container called ~/elastix (which is equivalent to /home/user/elastix). Thus you can modify the code, config and registration parameters on the host machine.
Note: All paths specified in the config files are now relative to the ~/elastix folder in the docker container (which is also the path/to/ElastixExperimentTracker on the local machine).
The docker container does not have access to the files on the local file system. To access files either need add the files to a bound volume, e.g. putting the in a subfolder of path/to/ElastixExperimentTracker, or by binding additional volumes.
The -v flag can be used to bind additional volumes using the syntax -v absolute/path/in/host/machine:absolute/path/in/container. Multiple -v flags can be used with a single run command.
docker run -it -v path/to/ElastixExperimentTracker:/home/appuser/elastix -v absolute/path/in/host/machine:absolute/path/in/container elastixdocker:v0
--rmif you want the container to be automatically deleted when excited the--rmflag can be used in thedocker runcommand. Use this if you are not planning to reconnect to a stopped container by usingdocker start <container ID>followed bydocker attach <container ID>.