FMRIPREP ValueError: 'desc' is not a recognized entity

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1

Hi everyone,

For many of our participants who I am running through fmriprep (version 20.2.1), I get this error message:

ValueError: ‘desc’ is not a recognized entity. If you’re sure you want to impose this constraint, set invalid_filters=‘allow’.

–skip-bids-validation --omp-nthreads 8 --nthreads 12 --mem_mb 30000 --skull-strip-template MNIPediatricAsym:cohort-4 --output-spaces MNIPediatricAsym:res-2:cohort-4 --fs-no-reconall --dummy-scans 6 --fs-license-file /ELS_BIDS_longitudinal/freesurfer_license/license.txt --fs-subjects-dir /ELS-T1/derivatives/freesurfer-6.0.1

I have checked the json files and compared them to those subjects who run successfully, so I’m not quite sure where to turn next to troubleshoot. I appreciate any advice.

Sincerely,
Jackie

2

Does the dataset validate properly? --skip-bids-validation might be hiding the root cause.

Assuming that your dataset is valid, we would need a full traceback to find where in the code this error is being raised, and the full command would dbe helpful, as would a listing of your dataset (e.g., tree /path/to/dataset).

3

Thank you for pointing this out! I realized there was an error in my path :woman_facepalming:

4

Edit: I updated to the docker to fMRIPrep 20.2.6, as well as updating fmriprep-docker with pip, and it is working now.

I have this error myself.
BIDS structure is valid.
I created a free surfer folder in derivatives, no luck.
I created a sub-01 inside that folder, also did not help.
Not sure where to go with this.

Should I instead report it on GitHub as the message says?

(base) Johns-iMac-Pro :: fmri/fmri_rs/code » ./fmriprep sub-01
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.8 -it -v /Users/john/.freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /Volumes/Data/Research/fmri/fmri_rs:/data:ro -v /Volumes/Data/Research/fmri/fmri_rs/derivatives:/out nipreps/fmriprep:20.2.3 /data /out participant --skull-strip-t1w=force --skip_bids_validation --participant-label sub-01 --mem_mb 5000 --nthreads 8 --output-spaces MNI152NLin2009cAsym
You are using fMRIPrep-20.2.3, and a newer version of fMRIPrep is available: 20.2.6.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
211107-17:01:18,872 nipype.workflow IMPORTANT:

    Running fMRIPREP version 20.2.3:
      * BIDS dataset path: /data.
      * Participant list: ['01'].
      * Run identifier: 20211107-170024_797f3e7e-646b-4416-90a6-2f6099ccf7ec.
      * Output spaces: MNI152NLin2009cAsym:res-native.
      * Pre-run FreeSurfer's SUBJECTS_DIR: /out/freesurfer.
Process Process-2:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/workflow.py", line 82, in build_workflow
    retval["workflow"] = init_fmriprep_wf()
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 64, in init_fmriprep_wf
    single_subject_wf = init_single_subject_wf(subject_id)
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/base.py", line 304, in init_single_subject_wf
    func_preproc_wf = init_func_preproc_wf(bold_file)
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/bold/base.py", line 206, in init_func_preproc_wf
    sbref_files = layout.get(return_type='file', **entities)
  File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 631, in get
    raise ValueError(msg + "If you're sure you want to impose "
ValueError: 'desc' is not a recognized entity. If you're sure you want to impose this constraint, set invalid_filters='allow'.
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues

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