Hi,
I'm using the mne-bids-pipeline for the preprocessing of my current data set and noticed that the eeg_reference specified in the config file only seems to be applied for the epoched data in _07_make_epochs.py but not for the raw/continuous data:
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# Set an EEG reference |
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if "eeg" in cfg.ch_types: |
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projection = True if cfg.eeg_reference == "average" else False |
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epochs.set_eeg_reference(cfg.eeg_reference, projection=projection) |
If I see it correctly, the raw/continuous data is only re-referenced (to average) in the case of using ica_use_icalabel:
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if cfg.ica_use_icalabel: |
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raw.set_eeg_reference("average", projection=True).apply_proj() |
But please correct me if I'm wrong.
For my preprocessing, I plan to add code to re-reference the raw/continuous data (to the reference specified in the config file) in our fork in _08a_apply_ica.py after applying the ica and before saving the raw data. If this is alo of interest for you I am happy to do a small PR upstream.
Best,
Judith
Hi,
I'm using the mne-bids-pipeline for the preprocessing of my current data set and noticed that the
eeg_referencespecified in the config file only seems to be applied for the epoched data in_07_make_epochs.pybut not for the raw/continuous data:mne-bids-pipeline/mne_bids_pipeline/steps/preprocessing/_07_make_epochs.py
Lines 204 to 207 in 687e4d3
If I see it correctly, the raw/continuous data is only re-referenced (to average) in the case of using
ica_use_icalabel:mne-bids-pipeline/mne_bids_pipeline/steps/preprocessing/_08a_apply_ica.py
Lines 217 to 218 in 687e4d3
But please correct me if I'm wrong.
For my preprocessing, I plan to add code to re-reference the raw/continuous data (to the reference specified in the config file) in our fork in
_08a_apply_ica.pyafter applying the ica and before saving the raw data. If this is alo of interest for you I am happy to do a small PR upstream.Best,
Judith