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.
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.,
Thank you for pointing this out! I realized there was an error in my path
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:
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.
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
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