Why does mne.minimum_norm.apply_inverse_raw() call _check_reference() when using only MEG channels?

Hi everyone,

My question is why does mne.minimum_norm.apply_inverse_raw() call _check_reference() even if I set eeg to False when computing the forward solution? mne.minimum_norm.apply_inverse_epochs_gen() does not call _check_reference().

For context: I am currently working with HCP data and MNE-HCP and for some reason when I load the data using:

files = hcp.io.file_mapping.get_file_paths(subject=subj, data_type='rest',
                                           output='raw', hcp_path=hcp_dir, run_index=0)

raw = mne.io.read_raw_bti(files[0], head_shape_fname=None, convert=False, preload=True)

all reference channels are set to ecg. Furthermore, I would like to use ica.find_bads_ecg() etc. to automatically detect ECG and EOG components. However, for the HCP data the channels were split into ‘ECG+’ and ‘ECG-’ and the same is true for VEOG and HEOG. Therefore, I made the following function to rename the channels and combine the +/- channels:

def set_ecg_eog_channels(raw):
    Set correct channel type for EEG/ECG/EOG channels.

    Operates in place.
    # somehow all channels have type ECG -> set to EEG first
    ecg_picks = mne.pick_types(raw.info, ecg=True)
    for pick in ecg_picks:
        ch_name = raw.info['ch_names'][pick]
        raw.set_channel_types({ch_name: 'eeg'})

    # set correct channel names for ECG
    ecg_ch_mapping = {'EEG 001': 'ECG+', 'EEG 004': 'ECG-'}
    mne.channels.rename_channels(raw.info, ecg_ch_mapping)

    # combine ECG+/-, VEOG+/-, and HEOG+/- into three channels
    # and set appropriate channel types

However, this sets the custom_ref_applied flag to True and as a result I cannot use apply_inverse_raw(). I am not really sure what the EEG reference is used for when I am only interested in MEG channels so can I simply set the flag to False using the following function? Or is there a reason why this would be a bad idea? I also was wondering if I maybe should call mne.set_eeg_reference() as well?

def _set_custom_ref_to_off(raw):

    from mne.io.constants import FIFF
    with raw.info._unlock():
        raw.info['custom_ref_applied'] = FIFF.FIFFV_MNE_CUSTOM_REF_OFF

Maybe @larsoner could have a look?


  • MNE version: 1.0.3
  • operating system: macOS

This seems like a bug. We should only check EEG ref if EEG will be used. Maybe in the code we need to move this check after we prune info to the set of channels to be used for example. Feel free to open a GitHub issue for this (or even better, try fixing it in a PR if you’re up for it!).

This also seems like a bug, feel free to open an issue on GitHub

This suggests that either 1) the channel types of these are not properly set to ECG/EOG, or 2) they are properly set but we don’t make use of this information properly (less likely). Feel free to open an issue about this, too…