Windows fmriprep-docker, cannot find FS license

Software Support
1

Summary of what happened:

I cannot seem to get my fmriprep-docker command to find my FS license file.

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

fmriprep-docker \
D:\data\things-fmri\ds004192 \
D:/data/try \
--participant-label 01 \
--fs-license-file C:\software\freesurfer\license.txt \
--fs-no-reconall \
--output-spaces MNI152NLin2009cAsym:res-2 fsaverage \
--output-spaces MNI152NLin2009cAsym:res-2 T1w fsaverage

Version:

25.2.3

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

Docker

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

Validated as part of OpenNeuro upload: OpenNeuro

Relevant log outputs (up to 20 lines):

ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an existing license file at several paths, in this order: 1) command line argument ``--fs-license-file``; 2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues.

Screenshots / relevant information:

2

Hi @monsterkilling and welcome to neurostars!

Your command looks off. The three positional arguments are bids_dir output_dir {participant}, and you do not have participant in your command (e.g., after D:/data/try). Also, you specify output-spaces twice. I also recommend not disabling FreeSurfer, and specifying a working directory with the -w (although that’s not directly related to your error).

I also notice you have different slash conventions (e.g., backslashes in D:\data\things-fmri\ds004192 and forward in D:/data/try). I am not a Windows user, and I think people who do user Windows have had luck by using a Linux-like environment (e.g., WSL). That might prove easier for you.

Best,
Steven