I’m not sure if this is what you mean:
C:\Users\rubin\fs-license
You should have a license.txt from FreeSurfer (License - Free Surfer Wiki). Wherever you save that, you should point to it with --fs-license-file.
Thank you all for your help and explanations @effigies, @jsein, and @Steven
I finally figured what the problem was and why when I typed “ls” in Ubuntu (20.04), it generated a message saying “No such file or directory”.
I’m using Windows, running the fMRIPrep-docker command on Ubuntu and needed to mount file systems in Linux for this to be identified.
Here’s my final code and hope it helps anyone who is or will be facing a similar problem or who reaches the end of this thread:
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hi effigies,
following the installation instruction, I tried to run the comment “fmriprep-docker”, and the errors showed like this: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get “http://%2Fvar%2Frun%2Fdocker.sock/v1.24/images/json?filters=%7B%22reference%22%3A%7B%22nipreps%2Ffmriprep%3A21.0.2%22%3Atrue%7D%7D”: dial unix /var/run/docker.sock: connect: permission denied
Downloading. This may take a while…
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’.
Could not detect memory capacity of Docker container.
Do you have permission to run docker?
then I tried with “sudo fmriprep-docker” the error came with “command not found”;
following your advice, i tried with the comments: find ~/.local -name fmriprep-docker, and it printed as here:
/home/shin/.local/bin/fmriprep-docker
how can I solve these problems? do you know which step went wrong? thx a lot in advance
Did you go through the Docker installation docs? It sounds like you probably skipped Post-installation steps for Linux | Docker Documentation
thx a lot!! I finished the post-installation steps then it worked!
Hello @effigies
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
It appears that your user doesn’t have permissions in docker. I would probably suggest seeking help on the Docker forums if Post-installation steps for Linux | Docker Documentation does not help.
Thank you for your reply.
Best,
Roya