Trouble installing fmriprep

Summary of what happened:

Hi, I am currently using this Stanford website to install fmriprep on my Windows computer with WSL 2: fMRIPrep tutorial: Running the docker image | Stanford Center for Reproducible Neuroscience. However, I get the following error when trying to run fMRIPrep.

I replace the given directories correctly with my own file directories (have checked numerous times) but I keep getting this error that my freesurfer.txt directory is incorrect (even though I copied the path straight from Windows). This is the error I receive: fmriprep-docker: error: Path should point to a file (or symlink of file): </Users/ragha/freesurfer.txt>. Can I receive some assistance on this?

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep-docker \
/Users/franklinfeingold/Desktop/BIDS_NKI_walkthrough/Nifti \
/Users/franklinfeingold/Desktop/BIDS_NKI_walkthrough/derivatives \
participant \
--participant-label 2475376 \
--fs-license-file /Users/franklinfeingold/freesurfer.txt


Environment (Docker, Singularity / Apptainer, custom installation):

Data formatted according to a validatable standard? Please provide the output of the validator:


Relevant log outputs (up to 20 lines):


Screenshots / relevant information:

Hi @Raghav_Pallapothu and welcome to neurostars!

For future posts like this, please use the Software Support category which prompts you for important information. You can see I edited your post to include the template, and you can edit your post to add in the missing information.

Please edit your command to be the modified command with your paths.


What is the contents of /Users/ragha/freesurfer.txt? The error indicates that fmriprep-docker cannot access the file.

That is the needed freesurfer license to start fmriprep.

Did you bind the freesurfer license path to the container before executing this command?

@chiuhoward fmriprep-docker creates a wrapper to mount drives and files, including the license. I am wondering if Windows notation is causing errors, since most testing is done on Unix filesystems. That is why I asked @Raghav_Pallapothu to provide his exact command.

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Yes, not sure why but I don’t know why my WSL can’t read my file directories.