Summary of what happened:
Hi there,
I’m trying to run fmriprep-docker.
Command used (and if a helper script was used, a link to the helper script or the command generated):
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=23.0.5 -it -v C:\Users\GoodGameBarTO5\Desktop\Labs\Spreng\freesurfer\license.txt:/opt/freesurfer/license.txt:ro -v C:\Users\GoodGameBarTO5\Desktop\Labs\Spreng\BIDS:/data:ro -v C:\Users\GoodGameBarTO5\Desktop\Labs\Spreng\fmriprep:/out -v C:\Users\GoodGameBarTO5\Desktop\Labs\Spreng\freesurfer:/opt/subjects -v C:\work:/scratch nipreps/fmriprep:23.0.2 /data /out participant --fs-no-reconall --skip-bids-validation --fs-subjects-dir /opt/subjects -w /scratch
Version:
23.0.2
Environment (Docker, Singularity, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
Relevant log outputs (up to 20 lines):
I am receiving the following error:
RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=23.0.5 -it -v C:\Users\GoodGameBarTO5\Desktop\Labs\Spreng\freesurfer\license.txt:/opt/freesurfer/license.txt:ro -v C:\Users\GoodGameBarTO5\Desktop\Labs\Spreng\BIDS:/data:ro -v C:\Users\GoodGameBarTO5\Desktop\Labs\Spreng\fmriprep:/out -v C:\Users\GoodGameBarTO5\Desktop\Labs\Spreng\freesurfer:/opt/subjects -v C:\work:/scratch nipreps/fmriprep:23.0.2 /data /out participant --fs-no-reconall --skip-bids-validation --fs-subjects-dir /opt/subjects -w /scratch
230516-23:41:51,364 nipype.workflow IMPORTANT:
Running fMRIPrep version 23.0.2
License NOTICE ##################################################
fMRIPrep 23.0.2
Copyright 2023 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 is also distributed as a Docker container image.
The bootstrapping 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.
#################################################################
230516-23:41:51,419 nipype.workflow IMPORTANT:
Building fMRIPrep's workflow:
* BIDS dataset path: /data.
* Participant list: ['0005'].
* Run identifier: 20230516-234132_e07bf190-6ccd-4b95-abf8-bf4de9f1483c.
* Output spaces: MNI152NLin2009cAsym:res-native.
* Pre-run FreeSurfer's SUBJECTS_DIR: /opt/subjects.
230516-23:41:52,480 nipype.workflow INFO:
B0 field inhomogeneity map will be estimated with the following 1 estimators: [<EstimatorType.PEPOLAR: 2>].
Process Process-2:
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/opt/conda/lib/python3.9/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/cli/workflow.py", line 115, in build_workflow
retval["workflow"] = init_fmriprep_wf()
File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py", line 92, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/base.py", line 428, in init_single_subject_wf
func_preproc_wf = init_func_preproc_wf(bold_file, has_fieldmap=has_fieldmap)
File "/opt/conda/lib/python3.9/site-packages/fmriprep/workflows/bold/base.py", line 287, in init_func_preproc_wf
sbref_files = layout.get(return_type="file", **sb_ents)
File "/opt/conda/lib/python3.9/site-packages/bids/layout/layout.py", line 629, 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
Screenshots / relevant information:
I’m wondering if anyone knows what’s going on with this or how to fix it? Any help would be much appreciated! Sorry if I’m a newbie!