Sun,

It is difficult to diagnose without your giving your specific inputs and its specific outputs. I think you are trying to run the Docker version, and Docker is successfully loading the program inside it, but you may not have specified the needed input arguments. I think the error is being printed from the program running inside the Docker, so it's leading you to run commands that are appropriate for the standalone (non-Docker) version, which won't work when you try to run them outside the Docker instance. 

I think you want to use something like

./run_mri_reface_docker.sh yourInput.nii desiredOutputDirectory

If you cannot get it working this way, please give more detail of your inputs and outputs, so that I can help further.

Best regards,
Chris Schwarz