Notch filter: picks < n_channels(67) got 67 -ERROR

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1

Hi Everyone!

  • MNE version: 0.24.1
  • operating system: Windows 10 Pro build number: 19041.1415

I tried to filter my raw data (fif file) using mne.filter.notch_filter .

The code:

 raws = mne.io.read_raw(filepath, preload=True)
 raw = mne.io.concatenate_raws(raws)
 emg_channel_pick = mne.pick_types(raw.info, emg=True) 
 sampling_rate = raw.info['sfreq']
 freqs = 50.0 
 raw_filtered = mne.filter.notch_filter(raw, sampling_rate, freqs, picks=emg_channel_pick)

I also tried using mne.pick_channels for the emg_channel_picks, or not using picks at all, or writing the channel names or type directly to the command, but always got the same error.

And the error message says:

Traceback (most recent call last):
  File "cmc_process.py", line 99, in <module>
    raw_filtered = mne.filter.notch_filter(raw, sampling_rate, freqs, picks='emg')
  File "<decorator-gen-105>", line 24, in notch_filter
  File "C:\Anaconda\lib\site-packages\mne\filter.py", line 1190, in notch_filter
    xf = filter_data(x, Fs, highs, lows, picks, filter_length, tb_2, tb_2,
  File "<decorator-gen-103>", line 24, in filter_data
  File "C:\Anaconda\lib\site-packages\mne\filter.py", line 815, in filter_data
    data = _check_filterable(data)
  File "C:\Anaconda\lib\site-packages\mne\filter.py", line 1374, in _check_filterable
    x = np.asanyarray(x)
  File "C:\Anaconda\lib\site-packages\numpy\core\_asarray.py", line 136, in asanyarray
    return array(a, dtype, copy=False, order=order, subok=True)
  File "C:\Anaconda\lib\site-packages\mne\io\base.py", line 807, in __getitem__
    return self._getitem(item)
  File "C:\Anaconda\lib\site-packages\mne\io\base.py", line 810, in _getitem
    sel, start, stop = self._parse_get_set_params(item)
  File "C:\Anaconda\lib\site-packages\mne\io\base.py", line 742, in _parse_get_set_params
    sel = _picks_to_idx(self.info, item[0])
  File "C:\Anaconda\lib\site-packages\mne\io\pick.py", line 1069, in _picks_to_idx
    raise ValueError('All picks must be < n_channels (%d), got %r'
ValueError: All picks must be < n_channels (67), got 67

Thank you for any help!

2

I can replicate the pb with:

from pathlib import Path
import mne

sample_dir = Path(mne.datasets.sample.data_path())
sample_fname = sample_dir / 'MEG' / 'sample' / 'sample_audvis_raw.fif'

raw = mne.io.read_raw_fif(sample_fname, preload=True)
raw.crop(tmax=60)
raw.set_channel_types(mapping={'EEG 001': 'ecg'})

emg_channel_pick = mne.pick_types(raw.info, emg=True) 
sampling_rate = raw.info['sfreq']
freqs = 50.0 
raw_filtered = mne.filter.notch_filter(raw, sampling_rate, freqs, picks=emg_channel_pick)

@fannidkovacs can you open an issue on github? at Issues · mne-tools/mne-python · GitHub

Alex

3

Thank you Alex! I did open an issue, and it got resolved very fast.

There’s a raw.notch_filter(...) option which i could’t find before, but it works as it should. The mne.filter.notch_filter is for np.ndarrays only.

Your comment was very helpful for me.