Hi Yarik,
The problem indeed seems to be that fmriprep-docker (and to a lesser extent mriqc ran in Docker) creates an output directory by default with root ownership, preventing a succesful datalad save for the annexed files due to permissions.
Do you think the other issue I posted (Configuring remotes on and pushing to Github & GIN) could be related to the same issue?
I will try your singularity suggestion, or work with our server admin to find a solution for the docker issue, and will keep you posted here!
Small issue to be corrected in the handbook 3.3. Walkthrough: Parallel ENKI preprocessing with fMRIprep — The DataLad Handbook - in the last command of the findoutmore box, the single quotes are missing after the --call-fmt option.
Thanks a ton again!
Cheers,
Lukas