Brainstorm raw (median nerve) dataset#

Here we compute the evoked from raw for the Brainstorm tutorial dataset. For comparison, see [1] and:

https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf

# Authors: Mainak Jas <mainak.jas@telecom-paristech.fr>
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import numpy as np

import mne
from mne.datasets.brainstorm import bst_raw
from mne.io import read_raw_ctf

print(__doc__)

tmin, tmax, event_id = -0.1, 0.3, 2  # take right-hand somato
reject = dict(mag=4e-12, eog=250e-6)

data_path = bst_raw.data_path()

raw_path = data_path / "MEG" / "bst_raw" / "subj001_somatosensory_20111109_01_AUX-f.ds"
# Here we crop to half the length to save memory
raw = read_raw_ctf(raw_path).crop(0, 120).load_data()
raw.plot()

# set EOG channel
raw.set_channel_types({"EEG058": "eog"})
raw.set_eeg_reference("average", projection=True)

# show power line interference and remove it
raw.compute_psd(tmax=60).plot(
    average=False, amplitude=False, picks="data", exclude="bads"
)
raw.notch_filter(np.arange(60, 181, 60), fir_design="firwin")

events = mne.find_events(raw, stim_channel="UPPT001")

# pick MEG channels
picks = mne.pick_types(
    raw.info, meg=True, eeg=False, stim=False, eog=True, exclude="bads"
)

# Compute epochs
epochs = mne.Epochs(
    raw,
    events,
    event_id,
    tmin,
    tmax,
    picks=picks,
    baseline=(None, 0),
    reject=reject,
    preload=False,
)

# compute evoked
evoked = epochs.average()

# remove physiological artifacts (eyeblinks, heartbeats) using SSP on baseline
evoked.add_proj(mne.compute_proj_evoked(evoked.copy().crop(tmax=0)))
evoked.apply_proj()

# fix stim artifact
mne.preprocessing.fix_stim_artifact(evoked)

# correct delays due to hardware (stim artifact is at 4 ms)
evoked.shift_time(-0.004)

# plot the result
evoked.plot(time_unit="s")

# show topomaps
evoked.plot_topomap(times=np.array([0.016, 0.030, 0.060, 0.070]), time_unit="s")

ds directory : /home/circleci/mne_data/MNE-brainstorm-data/bst_raw/MEG/bst_raw/subj001_somatosensory_20111109_01_AUX-f.ds
    res4 data read.
    hc data read.
    Separate EEG position data file not present.
    Quaternion matching (desired vs. transformed):
       0.84   69.49    0.00 mm <->    0.84   69.49   -0.00 mm (orig :  -44.30   51.45 -252.43 mm) diff =    0.000 mm
      -0.84  -69.49    0.00 mm <->   -0.84  -69.49   -0.00 mm (orig :   46.28  -53.58 -243.47 mm) diff =    0.000 mm
      86.41    0.00    0.00 mm <->   86.41    0.00    0.00 mm (orig :   63.60   55.82 -230.26 mm) diff =    0.000 mm
    Coordinate transformations established.
    Reading digitizer points from ['/home/circleci/mne_data/MNE-brainstorm-data/bst_raw/MEG/bst_raw/subj001_somatosensory_20111109_01_AUX-f.ds/subj00111092011.pos']...
    Polhemus data for 3 HPI coils added
    Device coordinate locations for 3 HPI coils added
Picked positions of 2 EEG channels from channel info
    2 EEG locations added to Polhemus data.
    Measurement info composed.
Finding samples for /home/circleci/mne_data/MNE-brainstorm-data/bst_raw/MEG/bst_raw/subj001_somatosensory_20111109_01_AUX-f.ds/subj001_somatosensory_20111109_01_AUX-f.meg4:
    System clock channel is available, checking which samples are valid.
    240 x 1800 = 432000 samples from 302 chs
Current compensation grade : 3
Reading 0 ... 144000  =      0.000 ...   120.000 secs...
Using qt as 2D backend.
EEG channel type selected for re-referencing
Adding average EEG reference projection.
1 projection items deactivated
Average reference projection was added, but has not been applied yet. Use the apply_proj method to apply it.
Removing 5 compensators from info because not all compensation channels were picked.
Effective window size : 1.707 (s)
Plotting power spectral density (dB=True).
Need more than one channel to make topography for eeg. Disabling interactivity.
Filtering raw data in 1 contiguous segment
Setting up band-stop filter

FIR filter parameters
---------------------
Designing a one-pass, zero-phase, non-causal bandstop filter:
- Windowed time-domain design (firwin) method
- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
- Lower transition bandwidth: 0.50 Hz
- Upper transition bandwidth: 0.50 Hz
- Filter length: 7921 samples (6.601 s)

[Parallel(n_jobs=1)]: Done  17 tasks      | elapsed:    0.1s
[Parallel(n_jobs=1)]: Done  71 tasks      | elapsed:    0.4s
[Parallel(n_jobs=1)]: Done 161 tasks      | elapsed:    0.9s
[Parallel(n_jobs=1)]: Done 287 tasks      | elapsed:    1.7s
66 events found on stim channel UPPT001
Event IDs: [1 2]
Not setting metadata
33 matching events found
Setting baseline interval to [-0.1, 0.0] s
Applying baseline correction (mode: mean)
0 projection items activated
No channels 'grad' found. Skipping.
Adding projection: axial--0.100-0.000-PCA-01 (exp var=51.3%)
Adding projection: axial--0.100-0.000-PCA-02 (exp var=19.2%)
No channels 'eeg' found. Skipping.
2 projection items deactivated
Created an SSP operator (subspace dimension = 2)
2 projection items activated
SSP projectors applied...
Removing 5 compensators from info because not all compensation channels were picked.
Removing 5 compensators from info because not all compensation channels were picked.
Removing 5 compensators from info because not all compensation channels were picked.

References#

Total running time of the script: (0 minutes 9.894 seconds)

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