Docker Community Forums

Share and learn in the Docker community.

Fmriprep-docker help

I am using the nipreps/fmriprep container in Docker and am having some issues.
I have confirmed that my data is in the necessary format but am still getting an error that says the path does not exist, when in fact it does.

I have posed this question on other (neuroimaging) forums but some have suggested it might be due to an issue with Docker and not the format of my MRI data.

I am running this through Ubuntu. Below is the command and the error.

sudo docker run nipreps/fmriprep /home/afton/Documents/bids_dataset/ /home/afton/Documents/derivatives/fmriprep/ participant --participant-label sub-01 -fs-license-file /home/afton/Documents/FreeSurfer/license.txt

`fmriprep: error: Path does not exist /home/afton/Documents/bids_dataset/ ’

Someone suggested that I should mount the data to Docker using the following command:
sudo docker -v /home/afton run nipreps/fmriprep /home/afton/Documents/bids_dataset/ /home/afton/Documents/derivatives/fmriprep/ participant --participant-label sub-01 -fs-license-file /home/afton/Documents/FreeSurfer/license.txt

When doing so, it seems Docker ignores the container (?) and an error occurs that it does not recognize the commands associated with nipreps/fmriprep.

Would any one have some suggestions?