def import_evokes(evokes_fname):
import importlib
import mne
mu.add_mmvt_code_root_to_path()
from src.preproc import meg
importlib.reload(meg)
opt_trans_files = glob.glob(
op.join(mu.get_parent_fol(evokes_fname), '*.fif'))
trans_files = meg.filter_trans_files(opt_trans_files)
trans_file = mu.select_one_file(trans_files,
template='*.fif',
files_desc='MRI-Head transformation')
args = mu.get_remote_subject_info_args()
evokes = mne.read_evokeds(evokes_fname)
events_keys = [ev.comment for ev in evokes]
meg.read_sensors_layout(mu.get_user(),
args,
info=evokes[0].info,
trans_file=trans_file)
meg.save_evokes_to_mmvt(evokes, events_keys, mu.get_user())
_addon().import_meg_sensors()
_addon().add_data_to_meg_sensors()
# _addon().load_all_panels()
_addon().show_meg_sensors()
def read_sensors_layout_args(mri_subject, args):
return meg.read_sensors_layout(mri_subject,
args,
pick_meg=False,
pick_eeg=True,
overwrite_sensors=args.overwrite_sensors,
raw_template=args.raw_template,
trans_file=args.trans_fname,
info_fname=args.info_fname,
read_info_file=args.read_info_file,
raw_fname=args.raw_fname)
def read_sensors_layout(mri_subject,
args=None,
overwrite_sensors=False,
raw_template='',
trans_file='',
info_fname='',
info=None,
read_info_file=True,
raw_fname=''):
return meg.read_sensors_layout(mri_subject,
args,
overwrite_sensors=overwrite_sensors,
pick_meg=False,
pick_eeg=True,
trans_file=trans_file,
info=info,
info_fname=info_fname,
read_info_file=read_info_file,
raw_template=raw_template,
raw_fname=raw_fname)
def read_eeg_sensors_layout(subject, mri_subject, args):
return meg.read_sensors_layout(subject, mri_subject, args, pick_meg=False, pick_eeg=True)
def analyze_meg(subject, seizure_time, seizure_len):
raw, evoked = None, None
meg_raw_fnames = [
op.join(MEG_ROOT, 'nmr01209_6213848_07',
'nmr01209_6213848_07_Resting_eeg_meg_ica-raw.fif'),
op.join(MEG_DIR, subject,
'nmr01209_6213848_07_Resting_eeg_meg_ica-raw.fif')
]
meg_raw_fname = [f for f in meg_raw_fnames if op.isfile(f)][0]
# empty_room_fname = '/space/megraid/77/MEG/noise/no_name/'
meg_raw_fname_seizure = op.join(MEG_DIR, subject,
'{}_meg_seizure-raw.fif'.format(subject))
meg_evoked_fname = op.join(MEG_DIR, subject,
'{}_meg_seizure-ave.fif'.format(subject))
eeg_evoked_fname = op.join(MEG_DIR, subject,
'{}_eeg_seizure-ave.fif'.format(subject))
meeg_evoked_fname = op.join(MEG_DIR, subject,
'{}_meeg_seizure-ave.fif'.format(subject))
if not op.isfile(meg_raw_fname_seizure):
raw = mne.io.read_raw_fif(meg_raw_fname)
raw.set_eeg_reference('average',
projection=True) # set EEG average reference
raw = raw.crop(seizure_time - 2, seizure_time + seizure_len)
raw.save(meg_raw_fname_seizure)
# raw.plot(block=True)
# raw.plot(butterfly=True, group_by='position')
meg.read_sensors_layout(subject,
info=raw.info,
overwrite_sensors=False)
eeg.read_sensors_layout(subject,
info=raw.info,
overwrite_sensors=False)
if not op.isfile(meg_evoked_fname) or not op.isfile(
eeg_evoked_fname) or not op.isfile(meeg_evoked_fname):
if raw is None:
raw = mne.io.read_raw_fif(meg_raw_fname_seizure)
evoked = mne.EvokedArray(raw.get_data(), raw.info, comment='seizure')
meeg_evoked = evoked.pick_types(meg=True, eeg=True)
mne.write_evokeds(meeg_evoked_fname, meeg_evoked)
eeg_evoked = evoked.pick_types(meg=False, eeg=True)
mne.write_evokeds(eeg_evoked_fname, eeg_evoked)
meg.save_evokes_to_mmvt(eeg_evoked, [1], subject, modality='eeg')
meg_evoked = evoked.pick_types(meg=True, eeg=False)
mne.write_evokeds(meg_evoked_fname, meg_evoked)
meg.save_evokes_to_mmvt(evoked, [1], subject, modality='meg')
meg.create_helmet_mesh(subject, overwrite_faces_verts=True)
eeg.create_helmet_mesh(subject, overwrite_faces_verts=True)
overwrite_source_bem = False
args = meg.read_cmd_args(
dict(
subject=subject,
function=
'make_forward_solution,calc_inverse_operator,calc_stc,calc_labels_avg_per_condition',
atlas='electrodes_labels',
evo_fname=meeg_evoked_fname,
# recreate_src_spacing='ico5',
# fwd_recreate_source_space=overwrite_source_bem,
# recreate_bem_solution=overwrite_source_bem,
contrast='seizure',
task='seizure',
raw_fname=meg_raw_fname_seizure,
use_empty_room_for_noise_cov=True,
empty_fname='empty_room_raw.fif',
# overwrite_fwd=True
overwrite_stc=False,
overwrite_labels_data=True,
# pick_meg=True, pick_eeg=False,
# fwd_usingMEG=True, fwd_usingEEG=False,
))
meg.call_main(args)
def read_eeg_sensors_layout(mri_subject, args):
return meg.read_sensors_layout(mri_subject,
args,
pick_meg=False,
pick_eeg=True,
overwrite_sensors=args.overwrite_sensors)