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 fmriprep.cli.run import main
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/__init__.py", line 17, in <module>
import bids
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/__init__.py", line 2, in <module>
from .layout import BIDSLayout, BIDSLayoutIndexer
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/__init__.py", line 1, in <module>
from .layout import BIDSLayout, Query
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/layout.py", line 34, in <module>
from .models import (Config, BIDSFile, DerivativeDatasets, Entity, Tag)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/layout/models.py", line 25, in <module>
from ..config import get_option
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/config.py", line 111, in <module>
reset_options(True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/config.py", line 93, in reset_options
_update_from_standard_locations()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/config.py", line 107, in _update_from_standard_locations
from_file(locs, False)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/bids/config.py", line 76, in from_file
if Path(f).exists():
File "/opt/conda/envs/fmriprep/lib/python3.10/pathlib.py", line 1290, in exists
self.stat()
File "/opt/conda/envs/fmriprep/lib/python3.10/pathlib.py", 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!
F.