03. Changing which channels are marked as “bad”

You can use MNE-BIDS to mark MEG or (i)EEG recording channels as “bad”, for example if the connected sensor produced mostly noise – or no signal at all.

Similarly, you can declare channels as “good”, should you discover they were incorrectly marked as bad.

# Authors: Richard Höchenberger <richard.hoechenberger@gmail.com>
# License: BSD (3-clause)

We will demonstrate how to mark individual channels as bad on the MNE “sample” dataset. After that, we will mark channels as good again.

Let’s start by importing the required modules and functions, reading the “sample” data, and writing it in the BIDS format.

import os.path as op
import mne
from mne_bids import BIDSPath, write_raw_bids, read_raw_bids, mark_bad_channels

data_path = mne.datasets.sample.data_path()
raw_fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw.fif')
bids_root = op.join(data_path, '..', 'MNE-sample-data-bids')
bids_path = BIDSPath(subject='01', session='01', task='audiovisual', run='01',
                     root=bids_root)

raw = mne.io.read_raw_fif(raw_fname, verbose=False)
raw.info['line_freq'] = 60  # Specify power line frequency as required by BIDS.
write_raw_bids(raw, bids_path=bids_path, overwrite=True, verbose=False)

Out:

/Users/hoechenberger/Development/mne-bids/mne_bids/utils.py:246: RuntimeWarning: No events found or provided. Please make sure to set channel type using raw.set_channel_types or provide events_data.
  warn('No events found or provided. Please make sure to'

BIDSPath(
root: /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids
datatype: meg
basename: sub-01_ses-01_task-audiovisual_run-01_meg.fif)

Read the (now BIDS-formatted) data and print a list of channels currently marked as bad.

raw = read_raw_bids(bids_path=bids_path, verbose=False)
print(f'The following channels are currently marked as bad:\n'
      f'    {", ".join(raw.info["bads"])}\n')

Out:

Opening raw data file /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Reading events from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv.
Reading channel info from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv.
/Users/hoechenberger/Development/mne-bids/mne_bids/read.py:246: RuntimeWarning: The unit for channel(s) STI 001, STI 002, STI 003, STI 004, STI 005, STI 006, STI 014, STI 015, STI 016 has changed from V to NA.
  raw.set_channel_types(channel_type_dict)
The following channels are currently marked as bad:
    MEG 2443, EEG 053

So currently, two channels are maked as bad: EEG 053 and MEG 2443. Let’s assume that through visual data inspection, we found that two more MEG channels are problematic, and we would like to mark them as bad as well. To do that, we simply add them to a list, which we then pass to mne_bids.mark_bad_channels():

bads = ['MEG 0112', 'MEG 0131']
mark_bad_channels(ch_names=bads, bids_path=bids_path, verbose=False)

Out:

Opening raw data file /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Reading 0 ... 166799  =      0.000 ...   277.714 secs...
Reading events from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv.
Reading channel info from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv.
/Users/hoechenberger/Development/mne-bids/mne_bids/read.py:246: RuntimeWarning: The unit for channel(s) STI 001, STI 002, STI 003, STI 004, STI 005, STI 006, STI 014, STI 015, STI 016 has changed from V to NA.
  raw.set_channel_types(channel_type_dict)
Processing channel MEG 0112:
    status: bad
    description: n/a
Processing channel MEG 0131:
    status: bad
    description: n/a

That’s it! Let’s verify the result.

raw = read_raw_bids(bids_path=bids_path, verbose=False)
print(f'After marking MEG 0112 and MEG 0131 as bad, the following channels '
      f'are now marked as bad:\n    {", ".join(raw.info["bads"])}\n')

Out:

Opening raw data file /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Reading events from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv.
Reading channel info from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv.
After marking MEG 0112 and MEG 0131 as bad, the following channels are now marked as bad:
    MEG 0112, MEG 0131, MEG 2443, EEG 053

As you can see, now a total of four channels is marked as bad: the ones that were already bad when we started – EEG 053 and MEG 2443 – and the two channels we passed to mne_bids.mark_bad_channels() – MEG 0112 and MEG 0131. This shows that marking bad channels via mne_bids.mark_bad_channels(), by default, is an additive procedure, which allows you to mark additional channels as bad while retaining the information about all channels that had previously been marked as bad.

If you instead would like to replace the collection of bad channels entirely, pass the argument overwrite=True:

bads = ['MEG 0112', 'MEG 0131']
mark_bad_channels(ch_names=bads, bids_path=bids_path, overwrite=True,
                  verbose=False)

raw = read_raw_bids(bids_path=bids_path, verbose=False)
print(f'After marking MEG 0112 and MEG 0131 as bad and passing '
      f'`overwrite=True`, the following channels '
      f'are now marked as bad:\n    {", ".join(raw.info["bads"])}\n')

Out:

Opening raw data file /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Reading 0 ... 166799  =      0.000 ...   277.714 secs...
Reading events from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv.
Reading channel info from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv.
Resetting status and description for all channels.
Processing channel MEG 0112:
    status: bad
    description: n/a
Processing channel MEG 0131:
    status: bad
    description: n/a
Opening raw data file /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Reading events from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv.
Reading channel info from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv.
After marking MEG 0112 and MEG 0131 as bad and passing `overwrite=True`, the following channels are now marked as bad:
    MEG 0112, MEG 0131

Lastly, if you’re looking for a way to mark all channels as good, simply pass an empty list as ch_names, combined with overwrite=True:

bads = []
mark_bad_channels(ch_names=bads, bids_path=bids_path, overwrite=True,
                  verbose=False)

raw = read_raw_bids(bids_path=bids_path, verbose=False)
print(f'After passing `ch_names=[]` and `overwrite=True`, the following '
      f'channels are now marked as bad:\n    {", ".join(raw.info["bads"])}\n')

Out:

Opening raw data file /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Reading 0 ... 166799  =      0.000 ...   277.714 secs...
Reading events from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv.
Reading channel info from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv.
Resetting status and description for all channels.
Opening raw data file /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_meg.fif...
    Read a total of 3 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
    Range : 25800 ... 192599 =     42.956 ...   320.670 secs
Ready.
Reading events from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_events.tsv.
Reading channel info from /Users/hoechenberger/mne_data/MNE-sample-data/../MNE-sample-data-bids/sub-01/ses-01/meg/sub-01_ses-01_task-audiovisual_run-01_channels.tsv.
After passing `ch_names=[]` and `overwrite=True`, the following channels are now marked as bad: