# Setup for reading the raw data
raw = fiff.Raw(raw_fname, verbose=False)
events = mne.find_events(raw, stim_channel='STI 014')
inverse_operator = read_inverse_operator(fname_inv)
raw.info['bads'] = ['MEG 2443', 'EEG 053']
# picks MEG gradiometers
picks = fiff.pick_types(raw.info, meg=True, eeg=False, eog=True,
stim=False, exclude='bads')
tmin, tmax = 0, 120 # use the first 120s of data
fmin, fmax = 4, 100 # look at frequencies between 4 and 100Hz
NFFT = 2048 # the FFT size (NFFT). Ideally a power of 2
label = mne.read_label(fname_label)
stc = compute_source_psd(raw, inverse_operator, lambda2=1. / 9., method="dSPM",
tmin=tmin, tmax=tmax, fmin=fmin, fmax=fmax,
pick_ori="normal", NFFT=NFFT, label=label)
stc.save('psd_dSPM')
###############################################################################
# View PSD of sources in label
import matplotlib.pyplot as plt
plt.plot(1e3 * stc.times, stc.data.T)
plt.xlabel('Frequency (Hz)')
plt.ylabel('PSD (dB)')
plt.title('Source Power Spectrum (PSD)')
plt.show()
eeg=False,
eog=True,
stim=False,
exclude='bads')
tmin, tmax = 0, 120 # use the first 120s of data
fmin, fmax = 4, 100 # look at frequencies between 4 and 100Hz
n_fft = 2048 # the FFT size (n_fft). Ideally a power of 2
label = mne.read_label(fname_label)
stc = compute_source_psd(raw,
inverse_operator,
lambda2=1. / 9.,
method="dSPM",
tmin=tmin,
tmax=tmax,
fmin=fmin,
fmax=fmax,
pick_ori="normal",
n_fft=n_fft,
label=label,
dB=True)
stc.save('psd_dSPM')
###############################################################################
# View PSD of sources in label
plt.plot(1e3 * stc.times, stc.data.T)
plt.xlabel('Frequency (Hz)')
plt.ylabel('PSD (dB)')
plt.title('Source Power Spectrum (PSD)')
plt.show()
eeg=False,
eog=True,
stim=False,
exclude='bads')
tmin, tmax = 0, 120 # use the first 120s of data
fmin, fmax = 4, 100 # look at frequencies between 4 and 100Hz
NFFT = 2048 # the FFT size (NFFT). Ideally a power of 2
label = mne.read_label(fname_label)
stc = compute_source_psd(raw,
inverse_operator,
lambda2=1. / 9.,
method="dSPM",
tmin=tmin,
tmax=tmax,
fmin=fmin,
fmax=fmax,
pick_normal=True,
NFFT=NFFT,
label=label)
stc.save('psd_dSPM')
###############################################################################
# View PSD of sources in label
import pylab as pl
pl.plot(1e3 * stc.times, stc.data.T)
pl.xlabel('Frequency (Hz)')
pl.ylabel('PSD (dB)')
pl.title('Source Power Spectrum (PSD)')
def intra(subj_list, fmin, fmax):
'''
Performs main process, including generation of inverse solution and PSD computation.
'''
for subj in subj_list:
print('Now beginning intra processing on ' + subj + '...\n') * 5
# Set function parameters
fname_raw = data_path + subj[:5] + '/' + subj
fname_fwd = data_path + subj[:5] + '/' + subj[:-4] + '-ico-4-fwd.fif'
# Load data
raw = fiff.Raw(fname_raw)
forward_meg = mne.read_forward_solution(fname_fwd)
# Estimate noise covariance from the raw data
precov = mne.compute_raw_data_covariance(raw, reject=dict(eog=150e-6))
write_cov(data_path + subj[:5] + '/' + subj[:-4] + '-cov.fif', precov)
# Find events from raw file
events = mne.find_events(raw, stim_channel='STI 014')
# Write events to file
mne.write_events(data_path + subj[:5] + '/' + subj[:-4] + '-eve.fif', events)
# Set up pick list:
include = []
exclude = raw.info['bads']
picks = fiff.pick_types(raw.info, meg=True, eeg=False, stim=True, eog=True, include=include, exclude=exclude)
# Read epochs and remove bad epochs
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, proj=True, picks=picks, baseline=(None, 0), preload=True, reject=dict(grad=4000e-13, mag=4e-12, eog=150e-6))
# Average epochs to produce an evoked dataset, then write to disk
evoked = epochs.average()
evoked.save(data_path + subj[:5] + '/' + subj[:-4] + '-ave.fif')
# Regularize noise cov
cov = mne.cov.regularize(precov, evoked.info, grad=0.05, mag=0.05, eeg=0.1, proj=True)
# Restrict forward solution as necessary for MEG
restricted_fwd = mne.fiff.pick_types_forward(forward_meg, meg=True, eeg=False)
# Make inverse operator
info = evoked.info
inverse_operator = make_inverse_operator(info, restricted_fwd, cov, loose=None, depth=0.8)
# Pull data for averaging later
epc_array = epochs.get_data()
# Compute the inverse solution
inv = apply_inverse(evoked, inverse_operator, lambda2, "dSPM", pick_normal=False)
inv.save(data_path + subj[:5] + '/' + subj[:-4] + '-inv.fif')
# picks MEG gradiometers
picks = fiff.pick_types(raw.info, meg=True, eeg=False, eog=True, stim=False, exclude=exclude)
# Compute source power spectral density and save to file
psd = compute_source_psd(raw, inverse_operator, method='dSPM', lambda2=lambda2, fmin=fmin, fmax=fmax, NFFT=2048)
psd.save(data_path + subj[:5] + '/' + subj[:-4] + '-psd.fif')
trans,
src=src,
bem=bem,
eeg=False,
verbose=True)
# Compute and apply inverse to PSD estimated using multitaper + Welch
noise_cov = mne.compute_raw_covariance(raw_erm, n_jobs=18)
inverse_operator = make_inverse_operator(raw.info,
forward=fwd,
noise_cov=noise_cov,
verbose=True)
stc_psd, evoked_psd = compute_source_psd(raw,
inverse_operator,
method='MNE',
dB=False,
return_sensor=True,
low_bias=True,
adaptive=True,
n_jobs=config.N_JOBS,
n_fft=n_fft,
verbose=True)
stc_psds.append(stc_psd)
evoked_psds.append(evoked_psd)
grand_ave_stc /= len(stc_psds)
grand_ave_evo = mne.grand_average(evoked_psds)
topos = dict()
stcs = dict()
topo_norm = grand_ave_evo.data.sum(axis=1, keepdims=True)
stc_norm = grand_ave_stc.sum()
# Normalize each sensor/source by the total power across freqs
for band, limits in defaults.bands.items():
data = evoked_psd.copy().crop(*limits).data.sum(axis=1, keepdims=True)