Thank you Paul, I am using fmriprep-32.1.4.simg, and built it using this command:

singularity build ./fmriprep-23.1.4.simg docker://nipreps/fmriprep:23.1.4

I use this command to run fMRIprep:

singularity run --nv --cleanenv -B <bids directory> -B <path to fmriprep_temp folder>  -B <path to scratch folder> -B <path to cache folder> <path to fmriprep-23.1.4.simg> -w <path to fmriprep_temp folder> --output-spaces {MNI152NLin2009cAsym:res-1,T1w:res-1} --ignore slicetiming --fs-license-file <path to freesurfer license.txt> <bids directory> <output directory> participant --participant_label <subj> --skip-bids-validation

The only error I am getting is for the freesurfer license file location: --fs-license-file <path to freesurfer license.txt>

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


thank you!!

L
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wighton, Paul <PWIGHTON@mgh.harvard.edu>
Sent: Monday, June 3, 2024 12:33 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer license
 
Hi Liz,

What fmriprep container are you using and what are the full commands that are not working?

Are you bind-mounting the freesurfer license file into the container via `singularity exec --bind`?

-Paul

________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ayoub, Lizbeth <layoub@mgh.harvard.edu>
Sent: Monday, June 3, 2024 11:48 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Freesurfer license

Hi,

I am using singularity to run fmriprep, and it seems that it is not recognizing the location of my freesurfer license ( it is a new license). I have tried all three options for location, and none work:

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

I appreciate any insights on how to fix this error :)

Thank you so much,

Liz











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