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
Hi Yarik,
Last update: after some tweaking of the singularity installation, everything works fine.
You may want to add to the handbook that wrapping fmriprep-docker in a datalad run command is not a viable option due to permission issues on multi-user systems?!
Thanks a ton for your help on this issue!
Best wishes,
Lukas
re fmriprep-docker – which version do you have? did you make use of --user option, see
'Developer options', 'Tools for testing and debugging FMRIPREP') g_dev.add_argument('--patch', nargs="+", metavar="PACKAGE=PATH", action=ToDict, help='local repository to use within container') g_dev.add_argument('--shell', action='store_true', help='open shell in image instead of running FMRIPREP') g_dev.add_argument('--config', metavar='PATH', action='store', type=os.path.abspath, help='Use custom nipype.cfg file') g_dev.add_argument('-e', '--env', action='append', nargs=2, metavar=('ENV_VAR', 'value'), help='Set custom environment variable within container') g_dev.add_argument('-u', '--user', action='store', help='Run container as a given user/uid. Additionally, group/gid can be' 'assigned, (i.e., --user <UID>:<GID>)') g_dev.add_argument('--network', action='store', help='Run container with a different network driver ' '("none" to simulate no internet connection)') g_dev.add_argument('--no-tty', action='store_true', help='Run docker without TTY flag -it') return parser
and also https://github.com/nipreps/fmriprep/issues/2098 (might need output directories to pre-created first?)
Thanks!
That could be an option too indeed, will test it!
Lukas
Hi Yarik,
I tried this option, but it resulted in errors during the fmriprep-docker run, so I will stick to the singularity method which works just fine!
Thanks for all the help on this!
Best wishes,
Lukas