ValuesError: Conflicting values found for entity 'run' in filename

[giulia-berto]

With version 20.2.0 I got this error (similar to that reported in issue #2 ):

  File "/usr/local/miniconda/bin/fmriprep", line 10, in <module>
    sys.exit(main())
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 17, in main
    parse_args()
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/parser.py", line 592, in parse_args
    config.from_dict(vars(opts))
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 612, in from_dict
    execution.load(settings)
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 218, in load
    cls.init()
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/config.py", line 448, in init
    re.compile(r"^\."),
  File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 155, in __init__
    indexer(self)
  File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 111, in __call__
    self._index_metadata()
  File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 427, in _index_metadata
    md_val))
bids.exceptions.BIDSConflictingValuesError: Conflicting values found for entity 'run' in filename /export/prod/5fce6985d89d01c47c5d0a9a/5fcea2b4d89d01b3be5d39ad/bids/sub-01/func/sub-01_task-rest_echo-3_run-01_bold.nii.gz (value='1') versus its JSON sidecar (value='01'). Please reconcile this discrepancy.```

[soichih]

Ref > bids-standard/pybids#687 (comment)

I've made an update to bl2bids script so that it will remove run from the json written out to bids directory (also convert run metadata field to an integer before using it as file name). Please try rerunning.

[giulia-berto]

thank you @soichih, that issue is solved now, however now there is another one:

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 84, 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 167, in init_func_preproc_wf
   config.loggers.warning(
AttributeError: type object 'loggers' has no attribute 'warning'

[soichih]

This looks like a fmriprep issue. Can you open a github issue here > https://github.com/nipreps/fmriprep/issues/new/choose

[giulia-berto]

ok done nipreps/fmriprep#2344

[giulia-berto]

that was already asked nipreps/fmriprep#2296
However I don't see any docker container with a more recent version than 20.2.0, I'll try with another version.

[effigies]

Apologies, the docker container is now nipreps/fmriprep, not poldracklab/fmriprep. We did not communicate this properly.

[giulia-berto]

Thanks, we are using nipreps/fmriprep now.