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DCAN-Labs / abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.
https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline
BSD 3-Clause "New" or "Revised" License
50 stars 19 forks source link

Access rights from Docker output #25

Closed MartinBa9210 closed 1 year ago

MartinBa9210 commented 4 years ago

Thanks for providing this great pipeline, works fine for me!

One comment, as it drives me nuts the first time, is accessing the Docker output on Linux machines. It turned out, that within Docker it run as root, but you might not be root any longer when you access your data.

To be sure about the correct rights put the flag --user "$(id -u):$(id -g)" to the docker options

so its:

docker run --rm --user "$(id -u):$(id -g)" \ -v /path/to/bids_dataset:/bids_input:ro \ -v /path/to/outputs:/output \ -v /path/to/freesurfer/license:/license \ dcanlabs/nhp-abcd-bids-pipeline /bids_input /output --freesurfer-license=/license [OPTIONS]

as a minimal command example.

Best, Martin

ericearl commented 4 years ago

This is a great observation, @MartinBa9210 , thanks! I will include this in the next revision.