Invalid Volume Specification?

[aureliooo]

Hi everyone! I'm new to fmriprep and have been having trouble getting it to run officially.

Though I follow the template of the command listed on the ReadTheDocs site,

"$ fmriprep-docker /path/to/data/dir /path/to/output/dir participant"

I keep getting an error that tells me I have an invalid volume specification and it quotes the path directory I used in my command. Both with the fmriprep-docker wrapper and through Docker itself.

Is there an obvious fix that I am missing?

[effigies]

Hi, can you share the exact command you're using?

[aureliooo]

I am trying both:

"fmriprep-docker C:\Users\Aurelio\Documents\rsfMRI\SocialBrain C:\Users\Aurelio\Documents\rsfMRI participant --participant_label sub-01"

and

"Docker run -it --rm -v C:\Users\Aurelio\Documents\rsfMRI\SocialBrain:/data:ro -v C:\Users\Aurelio\Documents\rsfMRI:/out -v C:\Users\Aurelio\Documents\rsfMRI\freesurfer\license.txt:\opt\freesurfer\license.txt poldracklab/fmriprep:latest \data /out/out participant --participant_label sub-01"

[effigies]

I believe with Docker for Windows, you may need to specify in Docker itself that the given directories may be mounted, but I'm not positive of that.

Could you provide the text of the error?

[chrisgorgo]

Make sure Drive C is made available in docker settings

While you at it better increase RAM available to Docker.

[aureliooo]

It says

"error response from daemon: invalid volume specification: 'C:\Users\Aurelio\Documents\rsfMRI\SocialBrain:/data:ro'."

[aureliooo]

@chrisfilo I am running Docker on Windows 10 (not the professional one), so I was instructed to download Docker Toolbox instead. And I don't see any settings like those anywhere. To my understanding, it only downloaded the Docker Quickstart Terminal for just command lines.

Thank you everyone for their help. I REALLY appreciate it!

[chrisgorgo]

It's been a while since I used Docker Toolbox, but try /c/Users/Aurelio/Documents/rsfMRI/SocialBrain:/data:ro

[aureliooo]

It gives me the same error of invalid volume specification except now it says 'C:\Users\Aurelio\Documents\rsfMRI\SocialBrain;C:\Program Files\Git\data;ro:/data:ro'

[chrisgorgo]

Could you try passing it directly to docker (modifying the command fmriprep-docker prints)?

[aureliooo]

Yes, and it gives me the same errors unfortunately :(

[chrisgorgo]

And you are running this fro PowerShell not something like Git Bash?

[aureliooo]

I am not completely sure. But I just tried it again by running PowerShell through the Windows command line and the same error came up.

[chrisgorgo]

I am out of ideas, but I think this is not related to fmriprep and you will most likely experience the same issues if trying to mount a volume in docker when using hello-world image.

[oesteban]

After a quick google, maybe:

• Invalid Volume Specification docker/cli#240 (comment)
• Setting COMPOSE_CONVERT_WINDOWS_PATHS=1 env variable Can't mount a volume on Windows 7 docker-archive/toolbox#607 (comment)

[aureliooo]

After setting COMPOSE_CONVERT_WINDOWS_PATHS=1, a new error pops up?? So maybe that means it's progressing along. Now it is saying "invalid reference format: repository name must be lowercase"

[oesteban]

Hi @aureliooo, did you finally resolve this?

Otherwise, could you please attach a more comprehensive log for this error?

[aureliooo]

Hi @oesteban

I didn't exactly resolve this because I never figured out how to fix that error. However, I moved to a mac and used Docker for Mac and haven't had any problems with that error since. Thank you.

[oesteban]

I see, let's close it for now and let anyone experiencing this reopen.