Fmriprep_docker and network drives

1

Hi

I am fairly new to docker and I have been successful in getting fmriprep working using docker (for Windows, but using linux containers). However, I can only run if my files are local, as my docker doesn’t recognize my mounted network drives.

docker run -ti –rm -v C:/data_dir:/data:ro
-v C:/out_dir:/out
-v freesurfer_license_path:/opt/freesurfer/license.txt
poldracklab/fmriprep:latest /data /out participant
–fs-license-file /opt/freesurfer/license.txt

It works beautifully if the files are local, however if I use the network paths, Docker pop asks me if I want to share and i log in using my computer credentials, but then I get error from Daemon: an error occurred while sharing drive.

I have spent a day trying to find solutions online, but have failed miserably. Does anyone have any suggestions and/or come across a similar issue?

Any advice would be super helpful!

Thanks
Poornima

2

This seems like a generic issue related to Docker. I do not know the solution, but seeking help in a broader forum such as https://github.com/docker/for-win/issues might help.

1 Like
3

Hi Chris

Thanks for your reply. Yes, I agree this might be a generic Docker issue. But the reason that I posted here was because I was hoping someone in this group would have had to use Docker (locally) and data on their cluster/server and can shed some light into my problem.

Thanks very much
Poornima

4

Doesn’t hurt! I hope you’ll find a solution.

5

Hi @ak_poorni did you find a solution to this problem? I am having the same issue with network drives…I am running fmriprep on datasets that are too large to copy the data locally.

6

@being_saige - No, I never did. I am just running fmriprep directly on the cluster now.

7

Maybe this could be helpful - https://forums.docker.com/t/how-to-access-a-windows-network-share/47467/2

8

Hello
I had a problem with the directory of my docker
therefore I tried to change the directory of my docker.
Unfortunately, I didnt do it in the right way and when I wanted to run the fmriprep-docker for one subject faced this error;

docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post “http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create”: dial unix /var/run/docker.sock: connect: permission denied.
See ‘docker run --help’.

I tried to remove docker to install it again but I wasn’t successful
the codes that I used;

docker system prune -a
docker images -a
docker rmi Image Image

faced the same error;

docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post “http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create”: dial unix /var/run/docker.sock: connect: permission denied.

I tried theses codes;

sudo apt-get purge docker-engine
sudo apt-get autoremove --purge docker-engine
rm -rf /var/lib/docker

wasnn’t able to remove the docker.

Actually I have 2 question;

1- How can I completely remove the current docker?
2- How can I install Docker in the path I want?

Because all my problems started when docker was installed in a predefined path that didn’t have enough storage space

I am appreciative of your time and help