Question on dss_line() usage

Hi, its awesome that there is an implementation of the ZAPline algorithm in Python! I’m trying to use it, but I somehow fail to remove the noise components with it. I’m convinced that I must be doing something obvious wrong - any idea what it may be?

I’m using Elekta MEG data (322 MEG channels, after Signal Space Separation) that show an artifact at 60Hz stemming from a presentation display. Here is its PSD:

Here’s the code I am running:

>>> import mne
>>> from meegkit.dss import dss_line
# read in the data with mne-python
>>> raw_fname = Path(datadir) / f'sub-{subject}/meg' / f'sub-{subject}_task-memento_proc-sss_meg.fif'
>>> raw = mne.io.read_raw_fif(raw_fname)
>>> raw.load_data()
>>> data, artifact = dss_line(raw._data.T, fline=60, sfreq=1000)
Power of components removed by DSS: 0.00

Putting the data back into the MNE Raw Object and visualizing the psd plot shows an almost identical profile, with the 60Hz component being pretty much unaffected.

Any idea what I might be doing wrong here? Thanks much in advance!

[nbara]

I can confirm that that was part of the problem. The other problem seems to be that your 60hz peak is not really at 60hz. Using 61Hz works well I think.

Here’s the code I used:

import mne
import matplotlib.pyplot as plt
from meegkit.dss import dss_line

raw = mne.io.read_raw('./examples/sub-xxx_task-memento_proc-sss_meg.fif', preload=True)

# First problem : be careful how you pick your data from Raw objects
print(f'raw._data shape: {raw._data.shape}')
data = raw.get_data(picks=['meg'])
print(f'raw.get_data() shape: {data.shape}')

raw.crop(60, 260)  # we don't need that much signal

# Only take MEG channels (same as raw.get_data(picks=['meg']))
meg_ch_idx = mne.pick_types(raw.info, meg=True)
data = raw.get_data(picks=meg_ch_idx)
# Second problem: the peak seems to be closer to 61 hz
clean, artifact = dss_line(data.T, fline=61, sfreq=1000, nremove=10)

# Plot before/after
f, ax = plt.subplots(2, 2)
raw.plot_psd(ax=ax[0, :], show=False, fmin=1, fmax=150)
raw._data[meg_ch_idx] = clean.T  # put clean data back in raw
raw.plot_psd(ax=ax[1, :], show=True, fmin=1, fmax=150)

[nbara]

I’ll have a look. There’s at least a couple of reasons I can think of.

Btw, just a quick comment, raw._data.T is probably not the best way to access the raw data (even though I’m guilty of using it myself sometimes), as it will include all kinds of system and misc channels (on top of the grad and mag channels).

raw.get_data(picks=['meg']) is probably safer.