Note

Click here to download the full example code

Plot channel-level thresholdsΒΆ

This example demonstrates how to use autoreject to find channel-wise thresholds.

# Author: Mainak Jas <mainak.jas@telecom-paristech.fr>
# License: BSD-3-Clause

Let us first load the raw data using mne.io.read_raw_fif().

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

data_path = sample.data_path()
raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'
raw = io.read_raw_fif(raw_fname, preload=True)

Out:

Opening raw data file /home/stefanappelhoff/mne_data/MNE-sample-data/MEG/sample/sample_audvis_filt-0-40_raw.fif...
    Read a total of 4 projection items:
        PCA-v1 (1 x 102)  idle
        PCA-v2 (1 x 102)  idle
        PCA-v3 (1 x 102)  idle
        Average EEG reference (1 x 60)  idle
    Range : 6450 ... 48149 =     42.956 ...   320.665 secs
Ready.
Reading 0 ... 41699  =      0.000 ...   277.709 secs...

We can extract the events (or triggers) for epoching our signal.

event_fname = data_path + ('/MEG/sample/sample_audvis_filt-0-40_raw-'
                           'eve.fif')
event_id = {'Auditory/Left': 1}
tmin, tmax = -0.2, 0.5
events = mne.read_events(event_fname)

Now that we have the events, we can extract the trials for the selection of channels defined by picks.

epochs = mne.Epochs(raw, events, event_id, tmin, tmax,
                    baseline=(None, 0),
                    reject=None, verbose=False, preload=True)

picks = mne.pick_types(epochs.info, meg='grad', eeg=False, stim=False,
                       eog=False, exclude='bads')

Now, we compute the channel-level thresholds using autoreject.compute_thresholds(). The method parameter will determine how we will search for thresholds over a range of potential candidates.

import numpy as np  # noqa
from autoreject import compute_thresholds  # noqa

# Get a dictionary of rejection thresholds
threshes = compute_thresholds(epochs, picks=picks, method='random_search',
                              random_state=42, augment=False,
                              verbose=True)

Out:

/home/stefanappelhoff/Desktop/bids/autoreject/autoreject/utils.py:66: UserWarning: 2 channels are marked as bad. These will be ignored. If you want them to be considered by autoreject please remove them from epochs.info["bads"].
  warnings.warn(
/home/stefanappelhoff/miniconda3/envs/autoreject/lib/python3.8/site-packages/mne/externals/tqdm/__init__.py:5: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
  if LooseVersion(__version__) < LooseVersion('4.36'):
/home/stefanappelhoff/miniconda3/envs/autoreject/lib/python3.8/site-packages/mne/externals/tqdm/__init__.py:5: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
  if LooseVersion(__version__) < LooseVersion('4.36'):

  0%|          | Computing thresholds ... : 0/203 [00:00<?,       ?it/s]
  0%|          | Computing thresholds ... : 1/203 [00:00<00:34,    5.78it/s]
  1%|          | Computing thresholds ... : 2/203 [00:00<00:31,    6.44it/s]
  1%|1         | Computing thresholds ... : 3/203 [00:00<00:29,    6.74it/s]
  2%|1         | Computing thresholds ... : 4/203 [00:00<00:29,    6.79it/s]
  2%|2         | Computing thresholds ... : 5/203 [00:00<00:28,    6.96it/s]
  3%|2         | Computing thresholds ... : 6/203 [00:00<00:27,    7.07it/s]
  3%|3         | Computing thresholds ... : 7/203 [00:00<00:27,    7.15it/s]
  4%|3         | Computing thresholds ... : 8/203 [00:01<00:26,    7.29it/s]
  4%|4         | Computing thresholds ... : 9/203 [00:01<00:26,    7.38it/s]
  5%|4         | Computing thresholds ... : 10/203 [00:01<00:25,    7.51it/s]
  5%|5         | Computing thresholds ... : 11/203 [00:01<00:25,    7.60it/s]
  6%|5         | Computing thresholds ... : 12/203 [00:01<00:24,    7.67it/s]
  6%|6         | Computing thresholds ... : 13/203 [00:01<00:24,    7.73it/s]
  7%|6         | Computing thresholds ... : 14/203 [00:01<00:24,    7.80it/s]
  7%|7         | Computing thresholds ... : 15/203 [00:01<00:24,    7.78it/s]
  8%|7         | Computing thresholds ... : 16/203 [00:02<00:23,    7.81it/s]
  8%|8         | Computing thresholds ... : 17/203 [00:02<00:23,    7.78it/s]
  9%|8         | Computing thresholds ... : 18/203 [00:02<00:23,    7.83it/s]
  9%|9         | Computing thresholds ... : 19/203 [00:02<00:23,    7.82it/s]
 10%|9         | Computing thresholds ... : 20/203 [00:02<00:23,    7.74it/s]
 10%|#         | Computing thresholds ... : 21/203 [00:02<00:23,    7.70it/s]
 11%|#         | Computing thresholds ... : 22/203 [00:02<00:23,    7.66it/s]
 11%|#1        | Computing thresholds ... : 23/203 [00:03<00:23,    7.65it/s]
 12%|#1        | Computing thresholds ... : 24/203 [00:03<00:23,    7.65it/s]
 12%|#2        | Computing thresholds ... : 25/203 [00:03<00:23,    7.64it/s]
 13%|#2        | Computing thresholds ... : 26/203 [00:03<00:23,    7.63it/s]
 13%|#3        | Computing thresholds ... : 27/203 [00:03<00:22,    7.70it/s]
 14%|#3        | Computing thresholds ... : 28/203 [00:03<00:22,    7.71it/s]
 14%|#4        | Computing thresholds ... : 29/203 [00:03<00:22,    7.72it/s]
 15%|#4        | Computing thresholds ... : 30/203 [00:03<00:22,    7.76it/s]
 15%|#5        | Computing thresholds ... : 31/203 [00:04<00:22,    7.79it/s]
 16%|#5        | Computing thresholds ... : 32/203 [00:04<00:21,    7.82it/s]
 16%|#6        | Computing thresholds ... : 33/203 [00:04<00:21,    7.85it/s]
 17%|#6        | Computing thresholds ... : 34/203 [00:04<00:21,    7.85it/s]
 17%|#7        | Computing thresholds ... : 35/203 [00:04<00:21,    7.87it/s]
 18%|#7        | Computing thresholds ... : 36/203 [00:04<00:21,    7.90it/s]
 18%|#8        | Computing thresholds ... : 37/203 [00:04<00:20,    7.93it/s]
 19%|#8        | Computing thresholds ... : 38/203 [00:04<00:20,    7.95it/s]
 19%|#9        | Computing thresholds ... : 39/203 [00:04<00:20,    7.97it/s]
 20%|#9        | Computing thresholds ... : 40/203 [00:05<00:20,    7.99it/s]
 20%|##        | Computing thresholds ... : 41/203 [00:05<00:20,    8.01it/s]
 21%|##        | Computing thresholds ... : 42/203 [00:05<00:20,    8.02it/s]
 21%|##1       | Computing thresholds ... : 43/203 [00:05<00:19,    8.03it/s]
 22%|##1       | Computing thresholds ... : 44/203 [00:05<00:19,    8.05it/s]
 22%|##2       | Computing thresholds ... : 45/203 [00:05<00:19,    8.03it/s]
 23%|##2       | Computing thresholds ... : 46/203 [00:05<00:19,    8.01it/s]
 23%|##3       | Computing thresholds ... : 47/203 [00:05<00:19,    8.02it/s]
 24%|##3       | Computing thresholds ... : 48/203 [00:06<00:19,    8.01it/s]
 24%|##4       | Computing thresholds ... : 49/203 [00:06<00:19,    8.01it/s]
 25%|##4       | Computing thresholds ... : 50/203 [00:06<00:19,    8.02it/s]
 25%|##5       | Computing thresholds ... : 51/203 [00:06<00:19,    8.00it/s]
 26%|##5       | Computing thresholds ... : 52/203 [00:06<00:18,    7.97it/s]
 26%|##6       | Computing thresholds ... : 53/203 [00:06<00:18,    8.00it/s]
 27%|##6       | Computing thresholds ... : 54/203 [00:06<00:18,    8.00it/s]
 27%|##7       | Computing thresholds ... : 55/203 [00:06<00:18,    8.02it/s]
 28%|##7       | Computing thresholds ... : 56/203 [00:07<00:18,    8.04it/s]
 28%|##8       | Computing thresholds ... : 57/203 [00:07<00:18,    8.03it/s]
 29%|##8       | Computing thresholds ... : 58/203 [00:07<00:18,    8.04it/s]
 29%|##9       | Computing thresholds ... : 59/203 [00:07<00:17,    8.02it/s]
 30%|##9       | Computing thresholds ... : 60/203 [00:07<00:17,    8.04it/s]
 30%|###       | Computing thresholds ... : 61/203 [00:07<00:17,    8.05it/s]
 31%|###       | Computing thresholds ... : 62/203 [00:07<00:17,    8.06it/s]
 31%|###1      | Computing thresholds ... : 63/203 [00:07<00:17,    8.08it/s]
 32%|###1      | Computing thresholds ... : 64/203 [00:08<00:17,    8.07it/s]
 32%|###2      | Computing thresholds ... : 65/203 [00:08<00:17,    8.08it/s]
 33%|###2      | Computing thresholds ... : 66/203 [00:08<00:16,    8.09it/s]
 33%|###3      | Computing thresholds ... : 67/203 [00:08<00:16,    8.09it/s]
 33%|###3      | Computing thresholds ... : 68/203 [00:08<00:16,    8.09it/s]
 34%|###3      | Computing thresholds ... : 69/203 [00:08<00:16,    8.10it/s]
 34%|###4      | Computing thresholds ... : 70/203 [00:08<00:16,    8.09it/s]
 35%|###4      | Computing thresholds ... : 71/203 [00:08<00:16,    8.10it/s]
 35%|###5      | Computing thresholds ... : 72/203 [00:09<00:16,    8.11it/s]
 36%|###5      | Computing thresholds ... : 73/203 [00:09<00:16,    8.11it/s]
 36%|###6      | Computing thresholds ... : 74/203 [00:09<00:15,    8.12it/s]
 37%|###6      | Computing thresholds ... : 75/203 [00:09<00:15,    8.12it/s]
 37%|###7      | Computing thresholds ... : 76/203 [00:09<00:15,    8.13it/s]
 38%|###7      | Computing thresholds ... : 77/203 [00:09<00:15,    8.13it/s]
 38%|###8      | Computing thresholds ... : 78/203 [00:09<00:15,    8.11it/s]
 39%|###8      | Computing thresholds ... : 79/203 [00:09<00:15,    8.13it/s]
 39%|###9      | Computing thresholds ... : 80/203 [00:10<00:15,    8.15it/s]
 40%|###9      | Computing thresholds ... : 81/203 [00:10<00:14,    8.15it/s]
 40%|####      | Computing thresholds ... : 82/203 [00:10<00:14,    8.15it/s]
 41%|####      | Computing thresholds ... : 83/203 [00:10<00:14,    8.16it/s]
 41%|####1     | Computing thresholds ... : 84/203 [00:10<00:14,    8.15it/s]
 42%|####1     | Computing thresholds ... : 85/203 [00:10<00:14,    8.15it/s]
 42%|####2     | Computing thresholds ... : 86/203 [00:10<00:14,    8.17it/s]
 43%|####2     | Computing thresholds ... : 87/203 [00:10<00:14,    8.16it/s]
 43%|####3     | Computing thresholds ... : 88/203 [00:11<00:14,    8.14it/s]
 44%|####3     | Computing thresholds ... : 89/203 [00:11<00:14,    8.13it/s]
 44%|####4     | Computing thresholds ... : 90/203 [00:11<00:13,    8.10it/s]
 45%|####4     | Computing thresholds ... : 91/203 [00:11<00:13,    8.11it/s]
 45%|####5     | Computing thresholds ... : 92/203 [00:11<00:13,    8.11it/s]
 46%|####5     | Computing thresholds ... : 93/203 [00:11<00:13,    8.11it/s]
 46%|####6     | Computing thresholds ... : 94/203 [00:11<00:13,    8.11it/s]
 47%|####6     | Computing thresholds ... : 95/203 [00:11<00:13,    8.13it/s]
 47%|####7     | Computing thresholds ... : 96/203 [00:11<00:13,    8.14it/s]
 48%|####7     | Computing thresholds ... : 97/203 [00:12<00:13,    8.14it/s]
 48%|####8     | Computing thresholds ... : 98/203 [00:12<00:12,    8.08it/s]
 49%|####8     | Computing thresholds ... : 99/203 [00:12<00:12,    8.09it/s]
 49%|####9     | Computing thresholds ... : 100/203 [00:12<00:12,    8.10it/s]
 50%|####9     | Computing thresholds ... : 101/203 [00:12<00:12,    8.11it/s]
 50%|#####     | Computing thresholds ... : 102/203 [00:12<00:12,    8.12it/s]
 51%|#####     | Computing thresholds ... : 103/203 [00:12<00:12,    8.07it/s]
 51%|#####1    | Computing thresholds ... : 104/203 [00:13<00:12,    8.08it/s]
 52%|#####1    | Computing thresholds ... : 105/203 [00:13<00:12,    8.09it/s]
 52%|#####2    | Computing thresholds ... : 106/203 [00:13<00:11,    8.09it/s]
 53%|#####2    | Computing thresholds ... : 107/203 [00:13<00:11,    8.09it/s]
 53%|#####3    | Computing thresholds ... : 108/203 [00:13<00:11,    8.02it/s]
 54%|#####3    | Computing thresholds ... : 109/203 [00:13<00:11,    8.01it/s]
 54%|#####4    | Computing thresholds ... : 110/203 [00:13<00:11,    8.02it/s]
 55%|#####4    | Computing thresholds ... : 111/203 [00:13<00:11,    8.03it/s]
 55%|#####5    | Computing thresholds ... : 112/203 [00:14<00:11,    8.04it/s]
 56%|#####5    | Computing thresholds ... : 113/203 [00:14<00:11,    8.05it/s]
 56%|#####6    | Computing thresholds ... : 114/203 [00:14<00:11,    8.07it/s]
 57%|#####6    | Computing thresholds ... : 115/203 [00:14<00:10,    8.07it/s]
 57%|#####7    | Computing thresholds ... : 116/203 [00:14<00:10,    8.09it/s]
 58%|#####7    | Computing thresholds ... : 117/203 [00:14<00:10,    8.07it/s]
 58%|#####8    | Computing thresholds ... : 118/203 [00:14<00:10,    8.05it/s]
 59%|#####8    | Computing thresholds ... : 119/203 [00:14<00:10,    8.04it/s]
 59%|#####9    | Computing thresholds ... : 120/203 [00:15<00:10,    8.01it/s]
 60%|#####9    | Computing thresholds ... : 121/203 [00:15<00:10,    8.00it/s]
 60%|######    | Computing thresholds ... : 122/203 [00:15<00:10,    8.00it/s]
 61%|######    | Computing thresholds ... : 123/203 [00:15<00:09,    8.01it/s]
 61%|######1   | Computing thresholds ... : 124/203 [00:15<00:09,    8.02it/s]
 62%|######1   | Computing thresholds ... : 125/203 [00:15<00:09,    8.01it/s]
 62%|######2   | Computing thresholds ... : 126/203 [00:15<00:09,    8.00it/s]
 63%|######2   | Computing thresholds ... : 127/203 [00:15<00:09,    8.02it/s]
 63%|######3   | Computing thresholds ... : 128/203 [00:16<00:09,    8.03it/s]
 64%|######3   | Computing thresholds ... : 129/203 [00:16<00:09,    8.03it/s]
 64%|######4   | Computing thresholds ... : 130/203 [00:16<00:09,    8.04it/s]
 65%|######4   | Computing thresholds ... : 131/203 [00:16<00:08,    8.05it/s]
 65%|######5   | Computing thresholds ... : 132/203 [00:16<00:08,    8.06it/s]
 66%|######5   | Computing thresholds ... : 133/203 [00:16<00:08,    7.99it/s]
 66%|######6   | Computing thresholds ... : 134/203 [00:16<00:08,    8.01it/s]
 67%|######6   | Computing thresholds ... : 135/203 [00:16<00:08,    8.00it/s]
 67%|######6   | Computing thresholds ... : 136/203 [00:17<00:08,    8.00it/s]
 67%|######7   | Computing thresholds ... : 137/203 [00:17<00:08,    8.00it/s]
 68%|######7   | Computing thresholds ... : 138/203 [00:17<00:08,    7.99it/s]
 68%|######8   | Computing thresholds ... : 139/203 [00:17<00:08,    7.98it/s]
 69%|######8   | Computing thresholds ... : 140/203 [00:17<00:07,    7.98it/s]
 69%|######9   | Computing thresholds ... : 141/203 [00:17<00:07,    7.98it/s]
 70%|######9   | Computing thresholds ... : 142/203 [00:17<00:07,    7.97it/s]
 70%|#######   | Computing thresholds ... : 143/203 [00:17<00:07,    7.98it/s]
 71%|#######   | Computing thresholds ... : 144/203 [00:18<00:07,    7.99it/s]
 71%|#######1  | Computing thresholds ... : 145/203 [00:18<00:07,    7.99it/s]
 72%|#######1  | Computing thresholds ... : 146/203 [00:18<00:07,    7.95it/s]
 72%|#######2  | Computing thresholds ... : 147/203 [00:18<00:07,    7.93it/s]
 73%|#######2  | Computing thresholds ... : 148/203 [00:18<00:06,    7.86it/s]
 73%|#######3  | Computing thresholds ... : 149/203 [00:18<00:06,    7.82it/s]
 74%|#######3  | Computing thresholds ... : 150/203 [00:18<00:06,    7.77it/s]
 74%|#######4  | Computing thresholds ... : 151/203 [00:19<00:06,    7.60it/s]
 75%|#######4  | Computing thresholds ... : 152/203 [00:19<00:06,    7.63it/s]
 75%|#######5  | Computing thresholds ... : 153/203 [00:19<00:06,    7.58it/s]
 76%|#######5  | Computing thresholds ... : 154/203 [00:19<00:06,    7.57it/s]
 76%|#######6  | Computing thresholds ... : 155/203 [00:19<00:06,    7.59it/s]
 77%|#######6  | Computing thresholds ... : 156/203 [00:19<00:06,    7.60it/s]
 77%|#######7  | Computing thresholds ... : 157/203 [00:19<00:06,    7.62it/s]
 78%|#######7  | Computing thresholds ... : 158/203 [00:19<00:05,    7.61it/s]
 78%|#######8  | Computing thresholds ... : 159/203 [00:20<00:05,    7.63it/s]
 79%|#######8  | Computing thresholds ... : 160/203 [00:20<00:05,    7.66it/s]
 79%|#######9  | Computing thresholds ... : 161/203 [00:20<00:05,    7.67it/s]
 80%|#######9  | Computing thresholds ... : 162/203 [00:20<00:05,    7.69it/s]
 80%|########  | Computing thresholds ... : 163/203 [00:20<00:05,    7.69it/s]
 81%|########  | Computing thresholds ... : 164/203 [00:20<00:05,    7.71it/s]
 81%|########1 | Computing thresholds ... : 165/203 [00:20<00:04,    7.72it/s]
 82%|########1 | Computing thresholds ... : 166/203 [00:20<00:04,    7.75it/s]
 82%|########2 | Computing thresholds ... : 167/203 [00:21<00:04,    7.74it/s]
 83%|########2 | Computing thresholds ... : 168/203 [00:21<00:04,    7.44it/s]
 83%|########3 | Computing thresholds ... : 169/203 [00:21<00:04,    7.46it/s]
 84%|########3 | Computing thresholds ... : 170/203 [00:21<00:04,    7.49it/s]
 84%|########4 | Computing thresholds ... : 171/203 [00:21<00:04,    7.51it/s]
 85%|########4 | Computing thresholds ... : 172/203 [00:21<00:04,    7.51it/s]
 85%|########5 | Computing thresholds ... : 173/203 [00:21<00:04,    7.46it/s]
 86%|########5 | Computing thresholds ... : 174/203 [00:22<00:03,    7.44it/s]
 86%|########6 | Computing thresholds ... : 175/203 [00:22<00:03,    7.46it/s]
 87%|########6 | Computing thresholds ... : 176/203 [00:22<00:03,    7.50it/s]
 87%|########7 | Computing thresholds ... : 177/203 [00:22<00:03,    7.49it/s]
 88%|########7 | Computing thresholds ... : 178/203 [00:22<00:03,    7.49it/s]
 88%|########8 | Computing thresholds ... : 179/203 [00:22<00:03,    7.51it/s]
 89%|########8 | Computing thresholds ... : 180/203 [00:22<00:03,    7.53it/s]
 89%|########9 | Computing thresholds ... : 181/203 [00:23<00:02,    7.55it/s]
 90%|########9 | Computing thresholds ... : 182/203 [00:23<00:02,    7.56it/s]
 90%|######### | Computing thresholds ... : 183/203 [00:23<00:02,    7.54it/s]
 91%|######### | Computing thresholds ... : 184/203 [00:23<00:02,    7.56it/s]
 91%|#########1| Computing thresholds ... : 185/203 [00:23<00:02,    7.57it/s]
 92%|#########1| Computing thresholds ... : 186/203 [00:23<00:02,    7.46it/s]
 92%|#########2| Computing thresholds ... : 187/203 [00:23<00:02,    7.49it/s]
 93%|#########2| Computing thresholds ... : 188/203 [00:23<00:02,    7.49it/s]
 93%|#########3| Computing thresholds ... : 189/203 [00:24<00:01,    7.52it/s]
 94%|#########3| Computing thresholds ... : 190/203 [00:24<00:01,    7.55it/s]
 94%|#########4| Computing thresholds ... : 191/203 [00:24<00:01,    7.57it/s]
 95%|#########4| Computing thresholds ... : 192/203 [00:24<00:01,    7.59it/s]
 95%|#########5| Computing thresholds ... : 193/203 [00:24<00:01,    7.60it/s]
 96%|#########5| Computing thresholds ... : 194/203 [00:24<00:01,    7.59it/s]
 96%|#########6| Computing thresholds ... : 195/203 [00:24<00:01,    7.60it/s]
 97%|#########6| Computing thresholds ... : 196/203 [00:24<00:00,    7.62it/s]
 97%|#########7| Computing thresholds ... : 197/203 [00:25<00:00,    7.47it/s]
 98%|#########7| Computing thresholds ... : 198/203 [00:25<00:00,    7.03it/s]
 98%|#########8| Computing thresholds ... : 199/203 [00:25<00:00,    6.98it/s]
 99%|#########8| Computing thresholds ... : 200/203 [00:25<00:00,    7.02it/s]
 99%|#########9| Computing thresholds ... : 201/203 [00:25<00:00,    6.98it/s]
100%|#########9| Computing thresholds ... : 202/203 [00:26<00:00,    7.02it/s]
100%|##########| Computing thresholds ... : 203/203 [00:26<00:00,    7.04it/s]
100%|##########| Computing thresholds ... : 203/203 [00:26<00:00,    7.76it/s]

Finally, let us plot a histogram of the channel-level thresholds to verify that the thresholds are indeed different for different sensors.

import matplotlib.pyplot as plt  # noqa
from autoreject import set_matplotlib_defaults  # noqa
set_matplotlib_defaults(plt)

unit = r'fT/cm'
scaling = 1e13

plt.figure(figsize=(6, 5))
plt.tick_params(axis='x', which='both', bottom='off', top='off')
plt.tick_params(axis='y', which='both', left='off', right='off')

plt.hist(scaling * np.array(list(threshes.values())), 30,
         color='g', alpha=0.4)
plt.xlabel('Threshold (%s)' % unit)
plt.ylabel('Number of sensors')
plt.xlim((100, 950))
plt.tight_layout()
plt.show()
plot channel thresholds

Total running time of the script: ( 0 minutes 26.868 seconds)

Gallery generated by Sphinx-Gallery

Fork me on GitHub