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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