source localization by MNE

https://www.nmr.mgh.harvard.edu/mne/0.14/auto_tutorials/plot_mne_dspm_source_localization.html

// An highlighted block
# https://www.nmr.mgh.harvard.edu/mne/0.14/auto_tutorials/plot_mne_dspm_source_localization.html

import numpy as np
import matplotlib.pyplot as plt

import mne
from mne.datasets import sample
from mne.minimum_norm import (make_inverse_operator, apply_inverse,
                              write_inverse_operator)

# data_path = sample.data_path()
# raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif'


raw_fname ='E:\\data-c\\mne_data\\MNE-sample-data\\MEG\\sample\\sample_audvis_filt-0-40_raw.fif'


raw = mne.io.read_raw_fif(raw_fname,preload=True)
raw.set_eeg_reference()  # set EEG average reference
events = mne.find_events(raw, stim_channel='STI 014')

event_id = dict(aud_r=1)  # event trigger and conditions
tmin = -0.2  # start of each epoch (200ms before the trigger)
tmax = 0.5  # end of each epoch (500ms after the trigger)
raw.info['bads'] = ['MEG 2443', 'EEG 053']
picks = mne.pick_types(raw.info, meg=True, eeg=False, eog=True,
                       exclude='bads')
baseline = (None, 0)  # means from the first instant to t = 0
reject = dict(grad=4000e-13, mag=4e-12, eog=150e-6)

epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True, picks=picks,
                    baseline=baseline, reject=reject)


noise_cov = mne.compute_covariance(
    epochs, tmax=0., method=['shrunk', 'empirical'])

fig_cov, fig_spectra = mne.viz.plot_cov(noise_cov, raw.info)

evoked = epochs.average()
evoked.plot()
evoked.plot_topomap(times=np.linspace(0.05, 0.15, 5), ch_type='mag')

# Show whitening
evoked.plot_white(noise_cov)

# Read the forward solution and compute the inverse operator
data_path='E:\\data-c\\mne_data\\MNE-sample-data'
fname_fwd = data_path + '\\MEG\\sample\\sample_audvis-meg-oct-6-fwd.fif'
fwd = mne.read_forward_solution(fname_fwd)

# Restrict forward solution as necessary for MEG
fwd = mne.pick_types_forward(fwd, meg=True, eeg=False)

# make an MEG inverse operator
info = evoked.info
inverse_operator = make_inverse_operator(info, fwd, noise_cov,
                                         loose=0.2, depth=0.8)

write_inverse_operator('sample_audvis-meg-oct-6-inv.fif',
                       inverse_operator,overwrite=True)

method = "dSPM"
snr = 3.
lambda2 = 1. / snr ** 2
stc = apply_inverse(evoked, inverse_operator, lambda2,
                    method=method, pick_ori=None)

# del fwd, inverse_operator, epochs  # to save memory

plt.plot(1e3 * stc.times, stc.data[::100, :].T)
plt.xlabel('time (ms)')
plt.ylabel('%s value' % method)
plt.show()

#--------------------右脑-----------------------------------------------
# vertno_max, time_max = stc.get_peak(hemi='rh')
#
# subjects_dir = data_path + '/subjects'
# brain = stc.plot(surface='inflated', hemi='rh', subjects_dir=subjects_dir,  initial_time=time_max,
#                  clim=dict(kind='value', lims=[8, 12, 15]),
#                 time_unit='s')
# brain.add_foci(vertno_max, coords_as_verts=True, hemi='rh', color='blue',
#                scale_factor=0.6)
# brain.show_view('lateral')
#
# print('--------------------------------------')
#
# fs_vertices = [np.arange(10242)] * 2
# morph_mat = mne.compute_morph_matrix('sample', 'fsaverage', stc.vertices,
#                                      fs_vertices, smooth=None,
#                                      subjects_dir=subjects_dir)
# stc_fsaverage = stc.morph_precomputed('fsaverage', fs_vertices, morph_mat)
# brain_fsaverage = stc_fsaverage.plot(surface='inflated', hemi='rh',
#                                      subjects_dir=subjects_dir,
#                                      clim=dict(kind='value', lims=[8, 12, 15]),
#                                      initial_time=time_max, time_unit='s')
# brain_fsaverage.show_view('lateral')

#--------------------------左脑-----------------------------------------------------

vertno_max, time_max = stc.get_peak(hemi='lh')

subjects_dir = data_path + '/subjects'
brain = stc.plot(surface='inflated', hemi='lh', subjects_dir=subjects_dir,  initial_time=time_max,
                 clim=dict(kind='value', lims=[8, 12, 15]),
                time_unit='s')
brain.add_foci(vertno_max, coords_as_verts=True, hemi='lh', color='blue',
               scale_factor=0.6)
brain.show_view('lateral')

print('--------------------------------')
#
# fs_vertices = [np.arange(10242)] * 2
# morph_mat = mne.compute_morph_matrix('sample', 'fsaverage', stc.vertices,
#                                      fs_vertices, smooth=None,
#                                      subjects_dir=subjects_dir)
# stc_fsaverage = stc.morph_precomputed('fsaverage', fs_vertices, morph_mat)
# brain_fsaverage = stc_fsaverage.plot(surface='inflated', hemi='lh',
#                                      subjects_dir=subjects_dir,
#                                      clim=dict(kind='value', lims=[8, 12, 15]),
#                                      initial_time=time_max, time_unit='s')
# brain_fsaverage.show_view('lateral')