def compute_sources(subject, run, mri_available=True):
epochs_fname = get_SAflow_bids(FOLDERPATH, subject, run, stage='epo')[1]
epochs = read_epochs(epochs_fname)
info = epochs.info
noise_fname = '/storage/Yann/saflow_DATA/saflow_bids/sub-06/ses-recording/meg/sub-06_ses-recording_NOISE_meg.ds'
noise_raw = read_raw_ctf(noise_fname, preload=True)
noise_raw.pick_channels(epochs.info['ch_names']) # Choose channels
cov = mne.compute_raw_covariance(noise_raw,
method='shrunk',
cv=5,
tmin=0,
tmax=0.8) #change tmin and tmax ?
src = mne.setup_source_space('sub-' + str(subject),
subjects_dir=subjects_dir,
add_dist=False)
fname_src_fsaverage = subjects_dir + '/fsaverage/bem/fsaverage-vol-5-src.fif'
surface = op.join(subjects_dir, 'sub-' + str(subject), 'bem',
'inner_skull.surf')
vol_src = mne.setup_volume_source_space(
'sub-' + str(subject),
subjects_dir=subjects_dir,
mri='aseg.mgz',
surface=surface) #,volume_label='Right-Pallidum')
trans = get_SAflow_bids(FOLDERPATH, subject, run, stage='epotrans')[1]
conductivity = (0.3, ) # for single layer
fwd_filename = get_SAflow_bids(FOLDERPATH, subject, run, stage='epofwd')[1]
#if not op.isfile(fwd_filename):
model = mne.make_bem_model(subject='sub-' + str(subject),
ico=4,
conductivity=conductivity,
subjects_dir=subjects_dir)
bem = mne.make_bem_solution(model)
fwd = mne.make_forward_solution(info, trans, vol_src, bem, eeg=False)
mne.write_forward_solution(fwd_filename, fwd, overwrite=True)
# else:
# fwd = mne.read_forward_solution(fwd_filename)
inverse_operator = make_inverse_operator(info, fwd, cov, loose=1)
snr = 1.0
lambda2 = 1.0 / snr**2
for j, epoch in enumerate(epochs):
print('Epoch {} of {}'.format(j, len(epochs)))
epoch = epoch[np.newaxis, ...]
epoch = EpochsArray(epoch, info)
epoch.pick_types(meg='mag')
if method == 'dSPM':
stc = apply_inverse_epochs(epoch,
inverse_operator,
lambda2,
method='dSPM')
src_fs = mne.read_source_spaces(fname_src_fsaverage)
morph = mne.compute_source_morph(inverse_operator['src'],
subject_from='sub-' +
str(subject),
subjects_dir=subjects_dir,
src_to=src_fs,
verbose=True)
stc_fsaverage = morph.apply(stc[0])
savepath = get_SAflow_bids(FOLDERPATH,
subject,
run,
stage='eposources')[1]
stc_fsaverage.save(savepath)
del stc_fsaverage
def compute_sources(s):
filenames = [s + '_Fast1',s + '_Fast2',s + '_Fast3',s + '_Fast4',
s + '_Slow1',s + '_Slow2',s + '_Slow3',s + '_Slow4']
for f in filenames:
for t in triggs:
epochs_fname = path + 'MEG_data/' + s + '/MEG_data_epoched_' + t + '/' + f + '.fif'
stc_fname = path +'source_rec/stc_' + t + '/'
epochs = read_epochs(epochs_fname)
epochs = epochs.copy().resample(600, npad='auto')
info = epochs.info
noise_raw = read_raw_fif(path + 'MEG_data/' + s + '/MEG_data_epoched/' + s + '_noise.fif',
preload=True)
noise_raw.pick_channels(epochs.info['ch_names']) # Choose channels
cov = mne.compute_raw_covariance(noise_raw,method='shrunk', cv=5, tmin = 0., tmax = 10.) #change tmin and tmax ?
src = mne.setup_source_space(s,subjects_dir=subjects_dir, add_dist=False)
fname_src_fsaverage = subjects_dir + '/fsaverage/bem/fsaverage-vol-5-src.fif'
surface = op.join(subjects_dir, s, 'bem', 'inner_skull.surf')
vol_src = mne.setup_volume_source_space(s, subjects_dir=subjects_dir,mri='aseg.mgz',
surface=surface)#,volume_label='Right-Pallidum')
trans = path + 'MEG_data/' + s + '/MEG_data_epoched/' + f + '-trans.fif'
conductivity = (0.3,) # for single layer
fwd_filename = path_meg+ f + '-fwd.fif'
#if not op.isfile(fwd_filename):
model = mne.make_bem_model(subject=s, ico=4,
conductivity=conductivity,
subjects_dir=subjects_dir)
bem = mne.make_bem_solution(model)
fwd = mne.make_forward_solution(info,trans,vol_src,bem,eeg=False)
mne.write_forward_solution(fwd_filename,fwd,overwrite=True)
# else:
# fwd = mne.read_forward_solution(fwd_filename)
inverse_operator = make_inverse_operator(info, fwd, cov,loose=1)
snr = 1.0
lambda2 = 1.0 / snr ** 2
for j, epoch in enumerate(epochs):
epoch = epoch[np.newaxis,...]
epoch = EpochsArray(epoch,info)
epoch.pick_types(meg='mag')
if method == 'dSPM':
stc = apply_inverse_epochs(epoch,inverse_operator,lambda2,method='dSPM')
src_fs = mne.read_source_spaces(fname_src_fsaverage)
morph = mne.compute_source_morph(
inverse_operator['src'], subject_from=s, subjects_dir=subjects_dir,
src_to=src_fs, verbose=True)
stc_fsaverage = morph.apply(stc[0])
savepath = path_stc + '/stc_block_' + t +'_volume/'
directory = os.path.dirname(savepath + s + '/')
if not os.path.exists(directory):
os.makedirs(directory)
else:
pass
stc_fsaverage.save(savepath + s + '/' + f + '_epoch_' + str(j))
del stc_fsaverage