Fmriprep issue with pybids_config.json

Dear experts,
I am running fmirprep like:

singularity run --cleanenv \
  fmriprep.simg \
  /data/BIDS /data/fmriprep_out \
  -w /data/work \
  participant \
  --participant-label sub-40713

(singularity version 3.4.1-4.2.ohpc.1.3.9)

And I am getting the following error:

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/bin/fmriprep", line 5, in <module>
    from import main
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/", line 17, in <module>
    import bids
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/", line 2, in <module>
    from .layout import BIDSLayout, BIDSLayoutIndexer
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/", line 1, in <module>
    from .layout import BIDSLayout, Query
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/", line 34, in <module>
    from .models import (Config, BIDSFile, DerivativeDatasets, Entity, Tag)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/", line 25, in <module>
    from ..config import get_option
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/", line 111, in <module>
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/", line 93, in reset_options
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/", line 107, in _update_from_standard_locations
    from_file(locs, False)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/", line 76, in from_file
    if Path(f).exists():
  File "/opt/conda/envs/fmriprep/lib/python3.10/", line 1290, in exists
  File "/opt/conda/envs/fmriprep/lib/python3.10/", line 1097, in stat
    return self._accessor.stat(self, follow_symlinks=follow_symlinks)
PermissionError: [Errno 13] Permission denied: '/home/fmriprep/pybids_config.json'

Any suggestion on how to fix it?
Thank you!

Hi @fpizzaga,

What version of fmriprep are you using?


Hi @Steven ,
I pull the latest, but using docker://poldracklab/fmriprep:latest, which was version 20.2.0.

I am now running fMRIPrep v23.1.4 (docker://nipreps/fmriprep:latest):

singularity run --cleanenv \
   fmriprep.simg \
   --anat-only \
   --fs-no-reconall \
   --skip_bids_validation \
   --notrack \
   -v \
   /data/BIDS/ \
   /data/fmriprep_out \
   participant \
   --participant-label sub-40713

It is stuck since ~ 30 mins and I am not getting any logs. Probably this is a different topic.
Thank you!

Yes, please only use the nipreps version. Also,

this flag is not recommended, see here.

If you only want to do anatomical, you can use sMRIPrep (which is what fMRIPrep calls upon internally).