qsiprep output owned by root

[treanus]

Dear developers,

thanks for providing qsiprep.

I'm using docker on linux. The output of qsiprep is owned by root. Can this be changed?

In fmriprep, when using the docker option "-u $(id -u)", the output is owned by the user running the docker.

However, when trying similarly to fmriprep, this gives an error with qsiprep: PermissionError: [Errno 13] Permission denied: '/scratch/20210713-130651_41b9d39c-4cf3-4db0-abf0-74ed7c89dbda'

Thank you in advance for any advise.

Kind regards, Stefan.

[mattcieslak]

Hi @treanus, we haven't optimized the user setup for docker since singularity is much more common. Until we have a good fix for this, I think you can docker run --rm -ti -v /my/outputs:/data --entrypoint bash pennbbl/qsiprep:0.14.2 and change the permissions to /data in that shell.

[cookpa]

I believe the error arises because docker is creating a new directory to be mounted to /scratch. If you do

docker run ... -u $(id -u):$(id -g) -v /some/scratch/path:/scratch pennbbl/qsiprep:0.14.2

and /some/scratch/path does not exist, docker will create it, owned by root.

However, if you create /some/scratch/path first, it will be mounted with the same uid and gid inside the container.