Hello,

I have tried to download mri-reface onto my linux CLI interface but am unable to go further than having the directory unzipped and coming across the following files.

mri_reface_CHANGES.txt  mri_reface_docker_README.txt  run_mri_reface_docker.sh
mri_reface_LICENSE.txt  mri_reface_docker_image

I tried running run_mri_reface_docker.sh by using bash run_mri_reface_docker.sh command but it gave me a bunch of text that told me to use mri_reface as a command with .nii file paths. However, running mri_reface gives me an error saying "Command not found".

Please let me know what I am doing wrong and how to actually run the mri_reface command because the documentation was not clear. I would be grateful if commands that I could use to load mri_reface onto my linux machine can be posted.

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