To set my montage correctly

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  • MNE version: 1.3.0
  • operating system: macOS 11.2

I want to set my montage with default ‘standard_1020’.

My data has 62 channels, corresponding to 64 channels but ‘M1’ and ‘M2’ are missing.
My channels are [‘FP1’, ‘FPZ’, ‘FP2’, ‘AF3’, ‘AF4’, ‘F7’, ‘F5’, ‘F3’, ‘F1’, ‘FZ’, ‘F2’, ‘F4’, ‘F6’, ‘F8’, ‘FT7’, ‘FC5’, ‘FC3’, ‘FC1’, ‘FCZ’, ‘FC2’, ‘FC4’, ‘FC6’, ‘FT8’, ‘T7’, ‘C5’, ‘C3’, ‘C1’, ‘CZ’, ‘C2’, ‘C4’, ‘C6’, ‘T8’, ‘TP7’, ‘CP5’, ‘CP3’, ‘CP1’, ‘CPZ’, ‘CP2’, ‘CP4’, ‘CP6’, ‘TP8’, ‘P7’, ‘P5’, ‘P3’, ‘P1’, ‘PZ’, ‘P2’, ‘P4’, ‘P6’, ‘P8’, ‘PO7’, ‘PO5’, ‘PO3’, ‘POZ’, ‘PO4’, ‘PO6’, ‘PO8’, ‘CB1’, ‘O1’, ‘OZ’, ‘O2’, ‘CB2’]

info = mne.create_info(ch_names, sfreq, ch_types='eeg')
# **samples** is a (62,37001) ndarray
raw = mne.io.RawArray(samples, info)
montage = mne.channels.make_standard_montage('standard_1020')
raw.set_montage(montage)

Then, when I try toraw.plot_psd_topo() it says ValueError: The following electrodes have overlapping positions, which causes problems during visualization: FP1, FPZ, FP2, FZ, FCZ, CZ, CPZ, PZ, POZ, CB1, OZ, CB2 but actually I use the default montage, why could this happen?

2

Hi @Chauncy ,

The channels that appear in the ValueError are channels that don’t have locations in the montage you set. I’m guessing that you set your montage to raw.set_montage(montage, on_missing="ignore") ?

From what I can tell, you will need to set the locations for all the electrodes before you call plot_topo.

There are a couple issues that you’ll need to fix. First, by default, set_montage is case sensitive and your channel names don’t match the case of the channel names in the standard_1020 template eeg montage (For example, it’s "Fp1" in the template montage, but your channel name is "FP1":

template_1020_montage = mne.channels.make_standard_montage("standard_1020")
print(template_1020_montage.ch_names)
# ['Fp1', 'Fpz', 'Fp2', 'AF9', 'AF7', 'AF5', 'AF3', .... 'A2']

Second, "CB1" and "CB2" are not in the standard 1020 montage. But you could use the "standard_1005" template montage, which has channels "P007" and "P008", which we know to be “aliases” for "CB1" and "CB2":

template_1005_montage = mne.channels.make_standard_montage('standard_1005')
print(template_1005_montage.ch_names)
# ['Fp1', 'Fpz', 'Fp2', ... , 'POO7',  'POO8', ..., 'A1', 'A2']
print(mne.io.constants.CHANNEL_LOC_ALIASES)
 # {'Cb1': 'POO7', ..., 'CB1': 'POO7', 'CB2': 'POO8', ..., }

So given your two issues, you can pass match_case=False and match_alias=True to set_montage to make channel matching case-insensitive, and to look for the known aliases we highlighted above:

raw.set_montage(template_1005_montage, match_case=False, match_alias=True)
psd = raw.compute_psd()
psd.plot_topo()

Note that raw.plot_psd_topo() is a legacy function and is not recommended. Please use raw.compute_psd().plot_topo() like I did in the code above.

Scott

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3

Thank you for helping me, this really works! :wink:

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