Brainstorm auditory tutorial dataset¶

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

http://neuroimage.usc.edu/brainstorm/Tutorials/Auditory

Experiment:

One subject, 2 acquisition runs 6 minutes each.

Each run contains 200 regular beeps and 40 easy deviant beeps.

Random ISI: between 0.7s and 1.7s seconds, uniformly distributed.

Button pressed when detecting a deviant with the right index finger.

The specifications of this dataset were discussed initially on the FieldTrip bug tracker.

References¶

[1]	Tadel F, Baillet S, Mosher JC, Pantazis D, Leahy RM. Brainstorm: A User-Friendly Application for MEG/EEG Analysis. Computational Intelligence and Neuroscience, vol. 2011, Article ID 879716, 13 pages, 2011. doi:10.1155/2011/879716

# Authors: Mainak Jas <mainak.jas@telecom-paristech.fr>
#          Eric Larson <larson.eric.d@gmail.com>
#          Jaakko Leppakangas <jaeilepp@student.jyu.fi>
#
# License: BSD (3-clause)

import os.path as op
import pandas as pd
import numpy as np

import mne
from mne import combine_evoked
from mne.minimum_norm import apply_inverse
from mne.datasets.brainstorm import bst_auditory
from mne.io import read_raw_ctf
from mne.filter import notch_filter, filter_data

print(__doc__)

To reduce memory consumption and running time, some of the steps are precomputed. To run everything from scratch change this to False. With use_precomputed = False running time of this script can be several minutes even on a fast computer.

use_precomputed = True

The data was collected with a CTF 275 system at 2400 Hz and low-pass filtered at 600 Hz. Here the data and empty room data files are read to construct instances of mne.io.Raw.

data_path = bst_auditory.data_path()

subject = 'bst_auditory'
subjects_dir = op.join(data_path, 'subjects')

raw_fname1 = op.join(data_path, 'MEG', 'bst_auditory',
                     'S01_AEF_20131218_01.ds')
raw_fname2 = op.join(data_path, 'MEG', 'bst_auditory',
                     'S01_AEF_20131218_02.ds')
erm_fname = op.join(data_path, 'MEG', 'bst_auditory',
                    'S01_Noise_20131218_01.ds')

In the memory saving mode we use preload=False and use the memory efficient IO which loads the data on demand. However, filtering and some other functions require the data to be preloaded in the memory.

preload = not use_precomputed
raw = read_raw_ctf(raw_fname1, preload=preload)
n_times_run1 = raw.n_times
mne.io.concatenate_raws([raw, read_raw_ctf(raw_fname2, preload=preload)])
raw_erm = read_raw_ctf(erm_fname, preload=preload)

Out:

ds directory : /home/ubuntu/mne_data/MNE-brainstorm-data/bst_auditory/MEG/bst_auditory/S01_AEF_20131218_01.ds
    res4 data read.
    hc data read.
    Separate EEG position data file read.
    Quaternion matching (desired vs. transformed):
       2.51   74.26    0.00 mm <->    2.51   74.26   -0.00 mm (orig :  -56.69   50.20 -264.38 mm) diff =    0.000 mm
      -2.51  -74.26    0.00 mm <->   -2.51  -74.26    0.00 mm (orig :   50.89  -52.31 -265.88 mm) diff =    0.000 mm
     108.63    0.00    0.00 mm <->  108.63    0.00   -0.00 mm (orig :   67.41   77.68 -239.53 mm) diff =    0.000 mm
    Coordinate transformations established.
    Reading digitizer points from [u'/home/ubuntu/mne_data/MNE-brainstorm-data/bst_auditory/MEG/bst_auditory/S01_AEF_20131218_01.ds/S01_20131218_01.pos']...
    Polhemus data for 3 HPI coils added
    Device coordinate locations for 3 HPI coils added
    5 extra points added to Polhemus data.
    Measurement info composed.
Finding samples for /home/ubuntu/mne_data/MNE-brainstorm-data/bst_auditory/MEG/bst_auditory/S01_AEF_20131218_01.ds/S01_AEF_20131218_01.meg4:
    System clock channel is available, checking which samples are valid.
    360 x 2400 = 864000 samples from 340 chs
Current compensation grade : 3
ds directory : /home/ubuntu/mne_data/MNE-brainstorm-data/bst_auditory/MEG/bst_auditory/S01_AEF_20131218_02.ds
    res4 data read.
    hc data read.
    Separate EEG position data file read.
    Quaternion matching (desired vs. transformed):
       2.64   74.60    0.00 mm <->    2.64   74.60    0.00 mm (orig :  -58.07   49.23 -263.11 mm) diff =    0.000 mm
      -2.64  -74.60    0.00 mm <->   -2.64  -74.60    0.00 mm (orig :   49.94  -53.82 -265.07 mm) diff =    0.000 mm
     108.24    0.00    0.00 mm <->  108.24   -0.00    0.00 mm (orig :   66.67   76.99 -243.39 mm) diff =    0.000 mm
    Coordinate transformations established.
    Reading digitizer points from [u'/home/ubuntu/mne_data/MNE-brainstorm-data/bst_auditory/MEG/bst_auditory/S01_AEF_20131218_02.ds/S01_20131218_01.pos']...
    Polhemus data for 3 HPI coils added
    Device coordinate locations for 3 HPI coils added
    5 extra points added to Polhemus data.
    Measurement info composed.
Finding samples for /home/ubuntu/mne_data/MNE-brainstorm-data/bst_auditory/MEG/bst_auditory/S01_AEF_20131218_02.ds/S01_AEF_20131218_02.meg4:
    System clock channel is available, checking which samples are valid.
    360 x 2400 = 864000 samples from 340 chs
Current compensation grade : 3
ds directory : /home/ubuntu/mne_data/MNE-brainstorm-data/bst_auditory/MEG/bst_auditory/S01_Noise_20131218_01.ds
    res4 data read.
    hc data read.
    Separate EEG position data file read.
    Quaternion matching (desired vs. transformed):
       0.00   80.00    0.00 mm <->    0.00   80.00    0.00 mm (orig :  -56.57   56.57 -270.00 mm) diff =    0.000 mm
       0.00  -80.00    0.00 mm <->    0.00  -80.00    0.00 mm (orig :   56.57  -56.57 -270.00 mm) diff =    0.000 mm
      80.00    0.00    0.00 mm <->   80.00   -0.00    0.00 mm (orig :   56.57   56.57 -270.00 mm) diff =    0.000 mm
    Coordinate transformations established.
    Polhemus data for 3 HPI coils added
    Device coordinate locations for 3 HPI coils added
    Measurement info composed.
Finding samples for /home/ubuntu/mne_data/MNE-brainstorm-data/bst_auditory/MEG/bst_auditory/S01_Noise_20131218_01.ds/S01_Noise_20131218_01.meg4:
    System clock channel is available, checking which samples are valid.
    15 x 4800 = 72000 samples from 301 chs
Current compensation grade : 3

Data channel array consisted of 274 MEG axial gradiometers, 26 MEG reference sensors and 2 EEG electrodes (Cz and Pz). In addition:

1 stim channel for marking presentation times for the stimuli

1 audio channel for the sent signal

1 response channel for recording the button presses

1 ECG bipolar

2 EOG bipolar (vertical and horizontal)

12 head tracking channels

20 unused channels

The head tracking channels and the unused channels are marked as misc channels. Here we define the EOG and ECG channels.

raw.set_channel_types({'HEOG': 'eog', 'VEOG': 'eog', 'ECG': 'ecg'})
if not use_precomputed:
    # Leave out the two EEG channels for easier computation of forward.
    raw.pick_types(meg=True, eeg=False, stim=True, misc=True, eog=True,
                   ecg=True)

For noise reduction, a set of bad segments have been identified and stored in csv files. The bad segments are later used to reject epochs that overlap with them. The file for the second run also contains some saccades. The saccades are removed by using SSP. We use pandas to read the data from the csv files. You can also view the files with your favorite text editor.

annotations_df = pd.DataFrame()
offset = n_times_run1
for idx in [1, 2]:
    csv_fname = op.join(data_path, 'MEG', 'bst_auditory',
                        'events_bad_0%s.csv' % idx)
    df = pd.read_csv(csv_fname, header=None,
                     names=['onset', 'duration', 'id', 'label'])
    print('Events from run {0}:'.format(idx))
    print(df)

    df['onset'] += offset * (idx - 1)
    annotations_df = pd.concat([annotations_df, df], axis=0)

saccades_events = df[df['label'] == 'saccade'].values[:, :3].astype(int)

# Conversion from samples to times:
onsets = annotations_df['onset'].values / raw.info['sfreq']
durations = annotations_df['duration'].values / raw.info['sfreq']
descriptions = annotations_df['label'].values

annotations = mne.Annotations(onsets, durations, descriptions)
raw.annotations = annotations
del onsets, durations, descriptions

Out:

Events from run 1:
     onset  duration  id label
   7625      2776   1   BAD
 142459       892   1   BAD
 216954       460   1   BAD
 345135      5816   1   BAD
 357687      1053   1   BAD
 409101      3736   1   BAD
 461110       179   1   BAD
 479866       426   1   BAD
 764914     11500   1   BAD
 798174      6589   1   BAD
846880      5383   1   BAD
858863      5136   1   BAD
Events from run 2:
     onset  duration  id    label
      9      5583   1      BAD
   9256      3114   1      BAD
  14287      3456   1      BAD
 116432       228   1      BAD
 134489      1329   1      BAD
 464527      4727   1      BAD
 494136      4519   1      BAD
 749288       189   1      BAD
 788623      7937   1      BAD
  21179         0   1  saccade
 72993         0   1  saccade
134527         0   1  saccade
196555         0   1  saccade
249894         0   1  saccade
343357         0   1  saccade
400771         0   1  saccade
450256         0   1  saccade
593101         0   1  saccade
733942         0   1  saccade
765939         0   1  saccade
789476         0   1  saccade
792852         0   1  saccade
833208         0   1  saccade
859869         0   1  saccade
862888         0   1  saccade

Here we compute the saccade and EOG projectors for magnetometers and add them to the raw data. The projectors are added to both runs.

saccade_epochs = mne.Epochs(raw, saccades_events, 1, 0., 0.5, preload=True,
                            reject_by_annotation=False)

projs_saccade = mne.compute_proj_epochs(saccade_epochs, n_mag=1, n_eeg=0,
                                        desc_prefix='saccade')
if use_precomputed:
    proj_fname = op.join(data_path, 'MEG', 'bst_auditory',
                         'bst_auditory-eog-proj.fif')
    projs_eog = mne.read_proj(proj_fname)[0]
else:
    projs_eog, _ = mne.preprocessing.compute_proj_eog(raw.load_data(),
                                                      n_mag=1, n_eeg=0)
raw.add_proj(projs_saccade)
raw.add_proj(projs_eog)
del saccade_epochs, saccades_events, projs_eog, projs_saccade  # To save memory

Out:

16 matching events found
0 projection items activated
Loading data for 16 events and 1201 original time points ...
1 bad epochs dropped
No gradiometers found. Forcing n_grad to 0
Adding projection: axial-saccade-PCA-01
    Read a total of 1 projection items:
        EOG-axial-998--0.200-0.200-PCA-01 (1 x 274)  idle
1 projection items deactivated
1 projection items deactivated

Visually inspect the effects of projections. Click on ‘proj’ button at the bottom right corner to toggle the projectors on/off. EOG events can be plotted by adding the event list as a keyword argument. As the bad segments and saccades were added as annotations to the raw data, they are plotted as well.

raw.plot(block=True)

../_images/sphx_glr_plot_brainstorm_auditory_001.png

Typical preprocessing step is the removal of power line artifact (50 Hz or 60 Hz). Here we notch filter the data at 60, 120 and 180 to remove the original 60 Hz artifact and the harmonics. The power spectra are plotted before and after the filtering to show the effect. The drop after 600 Hz appears because the data was filtered during the acquisition. In memory saving mode we do the filtering at evoked stage, which is not something you usually would do.

if not use_precomputed:
    meg_picks = mne.pick_types(raw.info, meg=True, eeg=False)
    raw.plot_psd(tmax=np.inf, picks=meg_picks)
    notches = np.arange(60, 181, 60)
    raw.notch_filter(notches)
    raw.plot_psd(tmax=np.inf, picks=meg_picks)

We also lowpass filter the data at 100 Hz to remove the hf components.

if not use_precomputed:
    raw.filter(None, 100., h_trans_bandwidth=0.5, filter_length='10s',
               phase='zero-double')

Epoching and averaging. First some parameters are defined and events extracted from the stimulus channel (UPPT001). The rejection thresholds are defined as peak-to-peak values and are in T / m for gradiometers, T for magnetometers and V for EOG and EEG channels.

tmin, tmax = -0.1, 0.5
event_id = dict(standard=1, deviant=2)
reject = dict(mag=4e-12, eog=250e-6)
# find events
events = mne.find_events(raw, stim_channel='UPPT001')

Out:

480 events found
Events id: [1 2]

The event timing is adjusted by comparing the trigger times on detected sound onsets on channel UADC001-4408.

sound_data = raw[raw.ch_names.index('UADC001-4408')][0][0]
onsets = np.where(np.abs(sound_data) > 2. * np.std(sound_data))[0]
min_diff = int(0.5 * raw.info['sfreq'])
diffs = np.concatenate([[min_diff + 1], np.diff(onsets)])
onsets = onsets[diffs > min_diff]
assert len(onsets) == len(events)
diffs = 1000. * (events[:, 0] - onsets) / raw.info['sfreq']
print('Trigger delay removed (μ ± σ): %0.1f ± %0.1f ms'
      % (np.mean(diffs), np.std(diffs)))
events[:, 0] = onsets
del sound_data, diffs

Out:

Trigger delay removed (μ ± σ): -14.0 ± 0.3 ms

We mark a set of bad channels that seem noisier than others. This can also be done interactively with raw.plot by clicking the channel name (or the line). The marked channels are added as bad when the browser window is closed.

raw.info['bads'] = ['MLO52-4408', 'MRT51-4408', 'MLO42-4408', 'MLO43-4408']

The epochs (trials) are created for MEG channels. First we find the picks for MEG and EOG channels. Then the epochs are constructed using these picks. The epochs overlapping with annotated bad segments are also rejected by default. To turn off rejection by bad segments (as was done earlier with saccades) you can use keyword reject_by_annotation=False.

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

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

Out:

480 matching events found
Created an SSP operator (subspace dimension = 2)
2 projection items activated

We only use first 40 good epochs from each run. Since we first drop the bad epochs, the indices of the epochs are no longer same as in the original epochs collection. Investigation of the event timings reveals that first epoch from the second run corresponds to index 182.

epochs.drop_bad()
epochs_standard = mne.concatenate_epochs([epochs['standard'][range(40)],
                                          epochs['standard'][182:222]])
epochs_standard.load_data()  # Resampling to save memory.
epochs_standard.resample(600, npad='auto')
epochs_deviant = epochs['deviant'].load_data()
epochs_deviant.resample(600, npad='auto')
del epochs, picks

Out:

Loading data for 480 events and 1441 original time points ...
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on MAG : [u'MLP52-4408']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'HEOG']
    Rejecting  epoch based on EOG : [u'HEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on MAG : [u'MLP52-4408']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'HEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'HEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'HEOG']
    Rejecting  epoch based on EOG : [u'HEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'HEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
    Rejecting  epoch based on EOG : [u'VEOG']
40 bad epochs dropped
Loading data for 40 events and 1441 original time points ...
Loading data for 40 events and 1441 original time points ...
80 matching events found
Created an SSP operator (subspace dimension = 2)
0 bad epochs dropped
Loading data for 75 events and 1441 original time points ...

The averages for each conditions are computed.

evoked_std = epochs_standard.average()
evoked_dev = epochs_deviant.average()
del epochs_standard, epochs_deviant

Typical preprocessing step is the removal of power line artifact (50 Hz or 60 Hz). Here we notch filter the data at 60, 120 and 180 to remove the original 60 Hz artifact and the harmonics. Normally this would be done to raw data (with mne.io.Raw.filter()), but to reduce memory consumption of this tutorial, we do it at evoked stage.

if use_precomputed:
    sfreq = evoked_std.info['sfreq']
    notches = [60, 120, 180]
    for evoked in (evoked_std, evoked_dev):
        evoked.data[:] = notch_filter(evoked.data, sfreq, notches)
        evoked.data[:] = filter_data(evoked.data, sfreq, l_freq=None,
                                     h_freq=100.)

Out:

Setting up band-stop filter
Filter length of 7920 samples (13.200 sec) selected
filter_length (7921) is longer than the signal (360), distortion is likely. Reduce filter length or filter a longer signal.
Setting up low-pass filter at 1e+02 Hz
h_trans_bandwidth chosen to be 25.0 Hz
Filter length of 158 samples (0.263 sec) selected
Setting up band-stop filter
Filter length of 7920 samples (13.200 sec) selected
filter_length (7921) is longer than the signal (360), distortion is likely. Reduce filter length or filter a longer signal.
Setting up low-pass filter at 1e+02 Hz
h_trans_bandwidth chosen to be 25.0 Hz
Filter length of 158 samples (0.263 sec) selected

Here we plot the ERF of standard and deviant conditions. In both conditions we can see the P50 and N100 responses. The mismatch negativity is visible only in the deviant condition around 100-200 ms. P200 is also visible around 170 ms in both conditions but much stronger in the standard condition. P300 is visible in deviant condition only (decision making in preparation of the button press). You can view the topographies from a certain time span by painting an area with clicking and holding the left mouse button.

evoked_std.plot(window_title='Standard', gfp=True)
evoked_dev.plot(window_title='Deviant', gfp=True)

Show activations as topography figures.

times = np.arange(0.05, 0.301, 0.025)
evoked_std.plot_topomap(times=times, title='Standard')
evoked_dev.plot_topomap(times=times, title='Deviant')

We can see the MMN effect more clearly by looking at the difference between the two conditions. P50 and N100 are no longer visible, but MMN/P200 and P300 are emphasised.

evoked_difference = combine_evoked([evoked_dev, -evoked_std], weights='equal')
evoked_difference.plot(window_title='Difference', gfp=True)

../_images/sphx_glr_plot_brainstorm_auditory_006.png

Source estimation. We compute the noise covariance matrix from the empty room measurement and use it for the other runs.

reject = dict(mag=4e-12)
cov = mne.compute_raw_covariance(raw_erm, reject=reject)
cov.plot(raw_erm.info)
del raw_erm

Out:

Using up to 149 segments
Number of samples used : 71520
[done]

The transformation is read from a file. More information about coregistering the data, see Interactive analysis with mne_analyze or mne.gui.coregistration().

trans_fname = op.join(data_path, 'MEG', 'bst_auditory',
                      'bst_auditory-trans.fif')
trans = mne.read_trans(trans_fname)

To save time and memory, the forward solution is read from a file. Set use_precomputed=False in the beginning of this script to build the forward solution from scratch. The head surfaces for constructing a BEM solution are read from a file. Since the data only contains MEG channels, we only need the inner skull surface for making the forward solution. For more information: Cortical surface reconstruction with FreeSurfer, mne.setup_source_space(), Creating the BEM meshes, mne.bem.make_watershed_bem().

if use_precomputed:
    fwd_fname = op.join(data_path, 'MEG', 'bst_auditory',
                        'bst_auditory-meg-oct-6-fwd.fif')
    fwd = mne.read_forward_solution(fwd_fname)
else:
    src = mne.setup_source_space(subject, spacing='ico4',
                                 subjects_dir=subjects_dir, overwrite=True)
    model = mne.make_bem_model(subject=subject, ico=4, conductivity=[0.3],
                               subjects_dir=subjects_dir)
    bem = mne.make_bem_solution(model)
    fwd = mne.make_forward_solution(evoked_std.info, trans=trans, src=src,
                                    bem=bem)

inv = mne.minimum_norm.make_inverse_operator(evoked_std.info, fwd, cov)
snr = 3.0
lambda2 = 1.0 / snr ** 2
del fwd

Out:

Reading forward solution from /home/ubuntu/mne_data/MNE-brainstorm-data/bst_auditory/MEG/bst_auditory/bst_auditory-meg-oct-6-fwd.fif...
    Reading a source space...
    Computing patch statistics...
    Patch information added...
    Distance information added...
    [done]
    Reading a source space...
    Computing patch statistics...
    Patch information added...
    Distance information added...
    [done]
    2 source spaces read
    Desired named matrix (kind = 3523) not available
    Read MEG forward solution (8196 sources, 270 channels, free orientations)
    Source spaces transformed to the forward solution coordinate frame
    Cartesian source orientations...
[done]
    Converting to surface-based source orientations...
    Average patch normals will be employed in the rotation to the local surface coordinates....
[done]
Computing inverse operator with 270 channels.
    Created an SSP operator (subspace dimension = 2)
estimated rank (mag): 268
Setting small MEG eigenvalues to zero.
Not doing PCA for MEG.
Total rank is 268
Creating the depth weighting matrix...
    270 magnetometer or axial gradiometer channels
    limit = 8033/8196 = 10.015871
    scale = 6.10585e-11 exp = 0.8
Computing inverse operator with 270 channels.
Creating the source covariance matrix
Applying loose dipole orientations. Loose value of 0.2.
Whitening the forward solution.
Adjusting source covariance matrix.
Computing SVD of whitened and weighted lead field matrix.
    largest singular value = 7.80635
    scaling factor to adjust the trace = 2.95615e+19

The sources are computed using dSPM method and plotted on an inflated brain surface. For interactive controls over the image, use keyword time_viewer=True. Standard condition.

stc_standard = mne.minimum_norm.apply_inverse(evoked_std, inv, lambda2, 'dSPM')
brain = stc_standard.plot(subjects_dir=subjects_dir, subject=subject,
                          surface='inflated', time_viewer=False, hemi='lh',
                          initial_time=0.1, time_unit='s')
del stc_standard, brain

../_images/sphx_glr_plot_brainstorm_auditory_009.png

Out:

Preparing the inverse operator for use...
    Scaled noise and source covariance from nave = 1 to nave = 80
    Created the regularized inverter
    Created an SSP operator (subspace dimension = 2)
    Created the whitener using a full noise covariance matrix (2 small eigenvalues omitted)
    Computing noise-normalization factors (dSPM)...
[done]
Picked 270 channels from the data
Computing inverse...
(eigenleads need to be weighted)...
combining the current components...
(dSPM)...
[done]
Updating smoothing matrix, be patient..
Smoothing matrix creation, step 1
Smoothing matrix creation, step 2
Smoothing matrix creation, step 3
Smoothing matrix creation, step 4
Smoothing matrix creation, step 5
Smoothing matrix creation, step 6
Smoothing matrix creation, step 7
Smoothing matrix creation, step 8
Smoothing matrix creation, step 9
Smoothing matrix creation, step 10
colormap: fmin=4.75e+00 fmid=5.62e+00 fmax=1.57e+01 transparent=1

Deviant condition.

stc_deviant = mne.minimum_norm.apply_inverse(evoked_dev, inv, lambda2, 'dSPM')
brain = stc_deviant.plot(subjects_dir=subjects_dir, subject=subject,
                         surface='inflated', time_viewer=False, hemi='lh',
                         initial_time=0.1, time_unit='s')
del stc_deviant, brain

../_images/sphx_glr_plot_brainstorm_auditory_010.png

Out:

Preparing the inverse operator for use...
    Scaled noise and source covariance from nave = 1 to nave = 75
    Created the regularized inverter
    Created an SSP operator (subspace dimension = 2)
    Created the whitener using a full noise covariance matrix (2 small eigenvalues omitted)
    Computing noise-normalization factors (dSPM)...
[done]
Picked 270 channels from the data
Computing inverse...
(eigenleads need to be weighted)...
combining the current components...
(dSPM)...
[done]
Updating smoothing matrix, be patient..
Smoothing matrix creation, step 1
Smoothing matrix creation, step 2
Smoothing matrix creation, step 3
Smoothing matrix creation, step 4
Smoothing matrix creation, step 5
Smoothing matrix creation, step 6
Smoothing matrix creation, step 7
Smoothing matrix creation, step 8
Smoothing matrix creation, step 9
Smoothing matrix creation, step 10
colormap: fmin=7.01e+00 fmid=8.16e+00 fmax=1.84e+01 transparent=1

Difference.

stc_difference = apply_inverse(evoked_difference, inv, lambda2, 'dSPM')
brain = stc_difference.plot(subjects_dir=subjects_dir, subject=subject,
                            surface='inflated', time_viewer=False, hemi='lh',
                            initial_time=0.15, time_unit='s')

../_images/sphx_glr_plot_brainstorm_auditory_011.png

Out:

Preparing the inverse operator for use...
    Scaled noise and source covariance from nave = 1 to nave = 155
    Created the regularized inverter
    Created an SSP operator (subspace dimension = 2)
    Created the whitener using a full noise covariance matrix (2 small eigenvalues omitted)
    Computing noise-normalization factors (dSPM)...
[done]
Picked 270 channels from the data
Computing inverse...
(eigenleads need to be weighted)...
combining the current components...
(dSPM)...
[done]
Updating smoothing matrix, be patient..
Smoothing matrix creation, step 1
Smoothing matrix creation, step 2
Smoothing matrix creation, step 3
Smoothing matrix creation, step 4
Smoothing matrix creation, step 5
Smoothing matrix creation, step 6
Smoothing matrix creation, step 7
Smoothing matrix creation, step 8
Smoothing matrix creation, step 9
Smoothing matrix creation, step 10
colormap: fmin=4.91e+00 fmid=5.74e+00 fmax=1.47e+01 transparent=1

Total running time of the script: ( 1 minutes 27.351 seconds)

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