fmriprep Freesurfer License Problems

What happened?

An error occurred when proceeding with the command.

What command did you use?

fmriprep-docker /Users/apple/Documents/project/HX/02/RawData
/Users/apple/Documents/project/HX/02/RawData/derivatives participant —participant-label C03
—fs-license-file /Users/apple/Documents/project/HX/02/license.txt —fs-no=reconall

What version of fMRIPrep are you running?

21.02

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

coconut:~ Duck$ fmriprep-docker /Users/apple/Documents/project/HX/02/RawData
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.16 -it -v /Users/apple/Documents/project/HX/02/RawData:/data:ro -v /Users/apple:/out nipreps/fmriprep:21.0.2 /data /out participant
/Users/apple/Documents/project/HX/02/RawData/derivatives participant —participant-label C03
—fs-license-file /Users/apple/Documents/project/HX/02/license.txt —[email protected]

	1: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)

	Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.


        Summary:                   Available Tasks:                     Available Modalities: 
        108 Files, 677.34MB        rest                                 MRI                   
        17 - Subjects              TODO: full task name for rest                              
        1 - Session                                                                           


	If you have any questions, please post on https://neurostars.org/tags/bids.

220713-05:00:54,82 nipype.workflow IMPORTANT:
	 Running fMRIPrep version 21.0.2

         License NOTICE ##################################################
         fMRIPrep 21.0.2
         Copyright 2021 The NiPreps Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software redistributes the versioneer Python package, which is
         Public domain source code.
         
         This software is also distributed as a Docker container image.
         The bootstraping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
220713-05:00:54,411 nipype.workflow IMPORTANT:
	 Building fMRIPrep's workflow:
           * BIDS dataset path: /data.
           * Participant list: ['C03', 'C05', 'C35', 'C38', 'C39', 'C42', 'T01', 'T03', 'T04', 'T06', 'T07', 'T08', 'T09', 'T10', 'T34', 'T36', 'T37'].
           * Run identifier: 20220713-050034_eb1abe48-7285-411c-9f71-b5b4a960d456.
           * Output spaces: MNI152NLin2009cAsym:res-native.
           * Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
220713-05:00:57,161 nipype.workflow INFO:
	 No single-band-reference found for sub-C03_task-rest_bold.nii.gz.
220713-05:00:57,322 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.961s.
220713-05:00:58,334 nipype.workflow INFO:
	 No single-band-reference found for sub-C05_task-rest_bold.nii.gz.
220713-05:00:58,486 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.961s.
220713-05:00:59,368 nipype.workflow INFO:
	 No single-band-reference found for sub-C35_task-rest_bold.nii.gz.
220713-05:00:59,520 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:00,805 nipype.workflow INFO:
	 No single-band-reference found for sub-C38_task-rest_bold.nii.gz.
220713-05:01:00,978 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:02,347 nipype.workflow INFO:
	 No single-band-reference found for sub-C39_task-rest_bold.nii.gz.
220713-05:01:02,605 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:04,31 nipype.workflow INFO:
	 No single-band-reference found for sub-C42_task-rest_bold.nii.gz.
220713-05:01:04,197 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:05,95 nipype.workflow INFO:
	 No single-band-reference found for sub-T01_task-rest_bold.nii.gz.
220713-05:01:05,252 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:05,985 nipype.workflow INFO:
	 No single-band-reference found for sub-T03_task-rest_bold.nii.gz.
220713-05:01:06,137 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:07,141 nipype.workflow INFO:
	 No single-band-reference found for sub-T04_task-rest_bold.nii.gz.
220713-05:01:07,313 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.961s.
220713-05:01:08,242 nipype.workflow INFO:
	 No single-band-reference found for sub-T06_task-rest_bold.nii.gz.
220713-05:01:08,404 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.961s.
220713-05:01:09,161 nipype.workflow INFO:
	 No single-band-reference found for sub-T07_task-rest_bold.nii.gz.
220713-05:01:09,327 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:10,394 nipype.workflow INFO:
	 No single-band-reference found for sub-T08_task-rest_bold.nii.gz.
220713-05:01:10,576 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:11,514 nipype.workflow INFO:
	 No single-band-reference found for sub-T09_task-rest_bold.nii.gz.
220713-05:01:11,691 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.961s.
220713-05:01:12,542 nipype.workflow INFO:
	 No single-band-reference found for sub-T10_task-rest_bold.nii.gz.
220713-05:01:12,716 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.961s.
220713-05:01:13,479 nipype.workflow INFO:
	 No single-band-reference found for sub-T34_task-rest_bold.nii.gz.
220713-05:01:13,636 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:14,651 nipype.workflow INFO:
	 No single-band-reference found for sub-T36_task-rest_bold.nii.gz.
220713-05:01:14,814 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:16,7 nipype.workflow INFO:
	 No single-band-reference found for sub-T37_task-rest_bold.nii.gz.
220713-05:01:16,182 nipype.workflow IMPORTANT:
	 BOLD series will be slice-timing corrected to an offset of 0.96s.
220713-05:01:21,667 nipype.workflow CRITICAL:
	 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

Additional information / screenshots

Jul 13 '22 05:07 yuketeng

It looks like you somehow got em-dashes instead of two dashes in your command. Try:

BASE=/Users/apple/Documents/project/HX/02
fmriprep-docker $BASE/RawData $BASE/RawData/derivatives participant \
    --participant-label C03 --fs-license-file $BASE/license.txt --fs-no-reconall

(BASE environment variable used for brevity.)

Jul 21 '22 13:07 effigies

@yuketeng please reopen if you are still having issues

Aug 30 '22 15:08 mgxd