raw.compute_psd() not working on acceleration data

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1

Hello!

My raw has acceleration channels (bio type) added to EEG data and I tried to use raw.compute_psd() on it. Tried to use raw.compute_psd(picks = []) with channel names, type and preselected channels with pick_channels() and none of them works.

I got different kinds of Errors:

ValueError: picks (NoneNone, treated as "data") yielded no channels, consider passing picks explicitly

or

ValueError: All picks must be < n_channels (67), got 67

or

ValueError: picks (['accx', 'accy', 'accz']) could not be interpreted as channel names (no channel "['accx', 'accy', 'accz']"), channel types (no type "accx"), or a generic type (just "all" or "data")

I had a similar issue with mne.filter.notch_filter and had to use raw.notch_filter(...) because mne.filter.notch_filter is for np.ndarray s only. Is this the case here as well? What could I use instead?

The legacy version mne.viz.plot_raw_psd(raw, picks=['accx', 'accy', 'accz']) works but with a slight bug (?). We work with 2 Hz movements, and on the psd plot it shows the peek slightly on the left.

p04_ckc_jobb_t1_02_psd
p04_ckc_jobb_t1_02_psd1000×350 13.4 KB

Thank you for any help!

2

Hello,

Using the stable version of MNE (1.3), compute_psd and its plot method does work if you provide the channel name explicitly.

from mne.datasets import sample
from mne.io import read_raw_fif


directory = sample.data_path() / "MEG" / "sample" 
raw = read_raw_fif(directory / "sample_audvis_raw.fif")
raw.pick_types(eog=True)
raw.load_data()
raw.set_channel_types({"EOG 061": "bio"})
raw.rename_channels({"EOG 061": "fakeAcce"})
spectrum = raw.compute_psd(picks="fakeAcce")
spectrum.plot(picks="fakeAcce")

Note that providing multiple channel as a list works too:

spectrum = raw.compute_psd(picks=["fakeAcce"])
spectrum.plot(picks=["fakeAcce"])

The channel name must be provided explicitly because bio channels are not considered as data channels. See this glossary entry: Glossary — MNE 1.3.1 documentation

Mathieu

4

Hi Mathieu,

Thank you for your answer! I’ve been using the stable verion, it seems like the problem was me not giving the explicit channel names for both the raw.compute_psd and .plot commands.

Thanks again,
Fanni