fMRIPrep: migrating from docker execution to fmriprep-docker

[effigies]

Your root user will have a different PATH than your own user, so fmriprep-docker will not show up to the root user. You can try:

sudo `which fmriprep-docker` ...

But that may not have the right PYTHONPATH environment to work with. The better solution is to give your user permission to run Docker images. See @oesteban’s comment here:

Manage Docker as a non-root user

Hi @Shengjie_Xu, What you are reporting is a consequence of the defaults when you install Docker (i.e., it doesn’t have to do with fmriprep or fmriprep-docker). Please have a look to their documentation if you want to be able to run docker as a non-root user (which is highly recommended). Incidentally, following up the guide will allow you to use the fmriprep-docker command.