Question: How does the _06a2_find_ica_artifacts detect EOG artifacts? #1005
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Description
I try to recreate the functionality of the mne_bids_pipeline _06a2_find_ica_artifacts step.
Here is my function:
def detect_eog_components(
ica: mne.preprocessing.ICA,
raw: mne.io.BaseRaw,
epochs: mne.Epochs,
verbose: bool = True
) -> mne.preprocessing.ICA:
"""
Detect and exclude EOG components from ICA using simulated EOG channels.
This function creates EOG epochs, finds bad EOG components using ICA,
and excludes them from the ICA solution.
Args:
ica: The ICA object to use for component detection.
raw: The unfiltered raw MNE data object.
epochs: The epochs object used for ICA fitting.
verbose: Whether to output additional information during processing.
Returns:
The modified ICA object with EOG components excluded.
"""
logger.info("Using simulated EOG channel to autoselect independent components")
eog_channels = ["Fp1", "Fp2"]
# Create EOG epochs
eog_epochs = mne.preprocessing.create_eog_epochs(raw, ch_name=eog_channels, baseline=(None, -0.2), verbose=verbose)
if len(eog_epochs):
if epochs.reject is not None:
eog_epochs.drop_bad(reject=epochs.reject)
# Find bad EOG components
eog_indices, eog_scores = ica.find_bads_eog(
eog_epochs,
ch_name=eog_channels,
threshold=3.0,
verbose=verbose
)
# Exclude detected EOG components
ica.exclude = eog_indices
return ica
Somehow I get a different number of eog epochs detected then with the mne_bids_pipeline. Is mne.preprocessing.create_eog_epochs
run on modified raw data in the pipeline?
Ideally we would need an extensive documentation that explain the steps in detail so it gets more transparent what they exactly do.
Thank you!!
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