TypeError: init_anat_preproc_wf() got an unexpected keyword argument 'bids_root'

1

This is with fmriprep 1.3.2:

/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/importlib/_bootstrap.py:219: RuntimeWarning: numpy.dtype size changed, may indicate binary incompatibility. Expected 96, got 88
  return f(*args, **kwds)
/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/site-packages/pytest.py' mode='r' encoding='utf-8'>
  imp.find_module('pytest')
/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__
  return f(*args, **kwds)
Process Process-2:
Traceback (most recent call last):
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/usr/local/Anaconda/envs/py3.6/lib/python3.6/multiprocessing/process.py", line 93, in run
    self._target(*self._args, **self._kwargs)
  File "/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/site-packages/fmriprep/cli/run.py", line 775, in build_workflow
    err_on_aroma_warn=opts.error_on_aroma_warnings,
  File "/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 218, in init_fmriprep_wf
    err_on_aroma_warn=err_on_aroma_warn,
  File "/gpfs/gsfs6/users/EDB/MErest/code/env-hpc/lib/python3.6/site-packages/fmriprep/workflows/base.py", line 462, in init_single_subject_wf
    template=template,
TypeError: init_anat_preproc_wf() got an unexpected keyword argument 'bids_root'
2

We split the anatomical processing components to an extra package. That one should be updated too:

pip install -U "smriprep>=0.1.1"

And once you are at it, it would time-saving to check on niworkflows and templateflow.

pip install -U "niworkflows<0.9.0a0,>=0.8.1" "templateflow<0.2.0a0,>=0.1.3"

Sorry for the inconvenience.

3

Thanks Oscar, very helpful. It went past that error and it’s running just fine so far. Thanks!
Anderson