Dear MNE developers,
My problem is related to the Maxfilter step of mne_bids_pipeline.
- MNE version: 1.5.1
- operating system: macOS 12.2.1
When running mne_bids_pipeline for some MEG data where I just recorded the position of the fiducials and HPI, using the following lines related to maxfilter step in config.py file:
find_flat_channels_meg = True
find_noisy_channels_meg = True
use_maxwell_filter = True
I get the following error message
preprocessing/_01_data_quality sub-02 run-01 A critical error occurred. The error message was: No digitization points found for dig_kinds=[4 (FIFFV_POINT_EXTRA), 3 (FIFFV_POINT_EEG)]
Aborting pipeline run. The traceback is:
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne_bids_pipeline/_run.py", line 55, in __mne_bids_pipeline_failsafe_wrapper__
out = memory.cache(func)(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne_bids_pipeline/_run.py", line 268, in wrapper
out_files = memorized_func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/joblib/memory.py", line 655, in __call__
return self._cached_call(args, kwargs)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/joblib/memory.py", line 598, in _cached_call
out, metadata = self.call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/joblib/memory.py", line 856, in call
output = self.func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py", line 89, in assess_data_quality
auto_scores = _find_bads_maxwell(
^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne_bids_pipeline/steps/preprocessing/_01_data_quality.py", line 194, in _find_bads_maxwell
) = mne.preprocessing.find_bad_channels_maxwell(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-472>", line 12, in find_bad_channels_maxwell
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne/preprocessing/maxwell.py", line 2629, in find_bad_channels_maxwell
params = _prep_maxwell_filter(
^^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-468>", line 12, in _prep_maxwell_filter
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne/preprocessing/maxwell.py", line 522, in _prep_maxwell_filter
origin = _check_origin(origin, info, coord_frame, disp=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne/bem.py", line 1162, in _check_origin
R, origin = fit_sphere_to_headshape(
^^^^^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-75>", line 10, in fit_sphere_to_headshape
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne/bem.py", line 998, in fit_sphere_to_headshape
radius, origin_head, origin_device = _fit_sphere_to_headshape(info, dig_kinds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-77>", line 12, in _fit_sphere_to_headshape
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne/bem.py", line 1091, in _fit_sphere_to_headshape
hsp = get_fitting_dig(info, dig_kinds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-76>", line 12, in get_fitting_dig
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne/bem.py", line 1044, in get_fitting_dig
return get_fitting_dig(info, ("extra", "eeg"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<decorator-gen-76>", line 12, in get_fitting_dig
File "/opt/anaconda3/envs/mne/lib/python3.11/site-packages/mne/bem.py", line 1060, in get_fitting_dig
raise ValueError(f"No digitization points found for dig_kinds={dig_kinds}")
I don’t get it if I put the following line in the config.py file:
mf_head_origin = [0,0,0]
but then the maxfiltering step seems to fail and the data is extremely noisy.
Thank you in advance for your help.
Fosca