Ploting Topographical maps

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  • MNE version: 1.6.1 in google colab
    I am trying to plot topographical map for MI Physionet dataset. The channel names in the montage and dataset vary eventhough I tried changing I am having digitization points error or wrong electrode locations plotted.I have provided the code snippet

original_names = [‘Fp1’, ‘AF7’, ‘AF3’, ‘F1’, ‘F3’, ‘F5’, ‘F7’, ‘FT7’, ‘FC5’, ‘FC3’, ‘FC1’, ‘C1’, ‘C3’, ‘C5’, ‘T7’,
‘TP7’, ‘CP5’, ‘CP3’, ‘CP1’, ‘P1’, ‘P3’, ‘P5’, ‘P7’, ‘P9’, ‘PO7’, ‘PO3’, ‘O1’, ‘Iz’, ‘Oz’, ‘POz’,
‘Pz’, ‘CPz’, ‘Fpz’, ‘Fp2’, ‘AF8’, ‘AF4’, ‘AFz’, ‘Fz’, ‘F2’, ‘F4’, ‘F6’, ‘F8’, ‘FT8’, ‘FC6’, ‘FC4’,
‘FC2’, ‘FCz’, ‘Cz’, ‘C2’, ‘C4’, ‘C6’, ‘T8’, ‘TP8’, ‘CP6’, ‘CP4’, ‘CP2’, ‘P2’, ‘P4’, ‘P6’, ‘P8’,
‘P10’, ‘PO8’, ‘PO4’, ‘O2’]
selected_electrodes = [‘FC5’, ‘FC3’, ‘FC1’,‘FCz’,‘FC2’, ‘FC4’, ‘FC6’, ‘C5’, ‘C3’, ‘C1’, ‘Cz’, ‘C2’, ‘C4’, ‘C6’,‘CP5’, ‘CP3’, ‘CP1’,‘CPz’, ‘CP2’, ‘CP4’, ‘CP6’]
subset_montage = mne.channels.make_standard_montage(‘biosemi64’)
subset_montage.ch_names = selected_electrodes
print(subset_montage.ch_names)
import mne

Define your selected channels

selected_channels = [‘Fc5.’, ‘Fc3.’, ‘Fc1.’, ‘Fcz.’, ‘Fc2.’, ‘Fc4.’, ‘Fc6.’, ‘C5…’, ‘C3…’, ‘C1…’, ‘Cz…’, ‘C2…’, ‘C4…’, ‘C6…’,‘Cp5.’, ‘Cp3.’, ‘Cp1.’, ‘Cpz.’, ‘Cp2.’, ‘Cp4.’, ‘Cp6.’]

Load or create your montage, for example:

montage = mne.channels.make_standard_montage(‘biosemi64’)

Pick only the selected channels from the montage

selected_montage = montage.copy().pick_channels(selected_channels)

Print the selected channels from the new montage

print(“Selected channels from the montage:”, selected_montage.ch_names)

2

Would you mind formatting your code appropriately so that it is easier to read? Also, please post the error message you are seeing.

3

The code and the error message as follows:
data1= mne.io.read_raw_edf(‘S002R03.edf’,preload=True)
data = mne.io.concatenate_raws([data1], on_mismatch=‘ignore’)
print(“Original Channel Names:”, data.ch_names)
selected_channels = [‘Fc5.’, ‘Fc3.’, ‘Fc1.’, ‘Fcz.’, ‘Fc2.’, ‘Fc4.’, ‘Fc6.’, ‘C5…’, ‘C3…’, ‘C1…’, ‘Cz…’, ‘C2…’, ‘C4…’, ‘C6…’,‘Cp5.’, ‘Cp3.’, ‘Cp1.’, ‘Cpz.’, ‘Cp2.’, ‘Cp4.’, ‘Cp6.’]
custom_mapping = {‘T1’:1}
(events_needed,event_dict1) = mne.events_from_annotations(data, event_id=custom_mapping)
print(event_dict1)
print(events_needed)
len(events_needed)
epochs = mne.Epochs(data, events_needed, tmin=0, tmax=4.1,proj=False, picks=selected_channels,
baseline=None, preload=True)
evoked = epochs[“1”].average()

original_names = [‘Fp1’, ‘AF7’, ‘AF3’, ‘F1’, ‘F3’, ‘F5’, ‘F7’, ‘FT7’, ‘FC5’, ‘FC3’, ‘FC1’, ‘C1’, ‘C3’, ‘C5’, ‘T7’,
‘TP7’, ‘CP5’, ‘CP3’, ‘CP1’, ‘P1’, ‘P3’, ‘P5’, ‘P7’, ‘P9’, ‘PO7’, ‘PO3’, ‘O1’, ‘Iz’, ‘Oz’, ‘POz’,
‘Pz’, ‘CPz’, ‘Fpz’, ‘Fp2’, ‘AF8’, ‘AF4’, ‘AFz’, ‘Fz’, ‘F2’, ‘F4’, ‘F6’, ‘F8’, ‘FT8’, ‘FC6’, ‘FC4’,
‘FC2’, ‘FCz’, ‘Cz’, ‘C2’, ‘C4’, ‘C6’, ‘T8’, ‘TP8’, ‘CP6’, ‘CP4’, ‘CP2’, ‘P2’, ‘P4’, ‘P6’, ‘P8’,
‘P10’, ‘PO8’, ‘PO4’, ‘O2’]
selected_electrodes = [‘FC5’, ‘FC3’, ‘FC1’,‘FCz’,‘FC2’, ‘FC4’, ‘FC6’, ‘C5’, ‘C3’, ‘C1’, ‘Cz’, ‘C2’, ‘C4’, ‘C6’,‘CP5’, ‘CP3’, ‘CP1’,‘CPz’, ‘CP2’, ‘CP4’, ‘CP6’]
montage = mne.channels.make_standard_montage(‘biosemi64’)
montage.ch_names = selected_electrodes
print(montage.ch_names)

epochs.ch_names, montage.ch_names

epochs.rename_channels({old_name: new_name for old_name, new_name in zip(epochs.ch_names, montage.ch_names)})
epochs.info.set_montage(montage1)
evoked = epochs[“1”].average()
Evoked.plot_topomap(ch_type=“eeg”, times=[0.5, 1,1.5,2])

#Error Message
Digitalization of points is not found