def calc_msit(args):
# python -m src.preproc.meg -s ep001 -m mg78 -a laus250 -t MSIT
# --contrast interference --t_max 2 --t_min -0.5 --data_per_task 1 --read_events_from_file 1
# --events_file_name {subject}_msit_nTSSS_interference-eve.txt --cleaning_method nTSSS
args = meg.read_cmd_args(
dict(
subject=args.subject,
mri_subject=args.mri_subject,
task='MSIT',
function=args.real_function,
data_per_task=True,
atlas='laus250',
contrast='interference',
cleaning_method='nTSSS',
t_min=-0.5,
t_max=2,
# calc_epochs_from_raw=True,
read_events_from_file=True,
# remote_subject_meg_dir='/autofs/space/sophia_002/users/DARPA-MEG/project_orig_msit',
events_file_name='{subject}_msit_nTSSS_interference-eve.txt',
reject=False,
# save_smoothed_activity=True,
# stc_t=1189,
morph_to_subject='fsaverage5',
extract_mode=['mean_flip', 'mean', 'pca_flip']))
meg.call_main(args)
def calc_rest(args):
# '-s hc029 -a laus125 -t rest -f calc_evoked,make_forward_solution,calc_inverse_operator --reject 0 --remove_power_line_noise 0 --windows_length 1000 --windows_shift 500 --remote_subject_dir "/autofs/space/lilli_001/users/DARPA-Recons/hc029"''
# '-s hc029 -a laus125 -t rest -f calc_stc,calc_labels_avg_per_condition --single_trial_stc 1 --remote_subject_dir "/autofs/space/lilli_001/users/DARPA-Recons/hc029"'
# '-s subject-name -a atlas-name -t rest -f rest_functions' --l_freq 8 --h_freq 13 --windows_length 500 --windows_shift 100
args = meg.read_cmd_args(dict(
subject=args.subject,
mri_subject=args.mri_subject,
atlas='laus125',
function='rest_functions',
task='rest',
cleaning_method='tsss',
reject=False, # Should be True here, unless you are dealling with bad data...
remove_power_line_noise=True,
l_freq=3, h_freq=80,
windows_length=500,
windows_shift=100,
inverse_method='MNE',
remote_subject_dir='/autofs/space/lilli_001/users/DARPA-Recons/{subject}',
# This properties are set automatically if task=='rest'
# calc_epochs_from_raw=True,
# single_trial_stc=True,
# use_empty_room_for_noise_cov=True,
# windows_num=10,
# baseline_min=0,
# baseline_max=0,
))
meg.call_main(args)
def calc_meg_epochs(args):
empty_fnames, cors, days = get_empty_fnames(args.subject[0], args.tasks,
args)
times = (-2, 4)
for task in args.tasks:
args = meg.read_cmd_args(
dict(subject=args.subject,
mri_subject=args.subject,
task=task,
remote_subject_dir=
'/autofs/space/lilli_001/users/DARPA-Recons/{subject}',
get_task_defaults=False,
fname_format='{}_{}_nTSSS-ica-raw'.format(
'{subject}', task.lower()),
empty_fname=empty_fnames[task],
function='calc_epochs,calc_evokes',
conditions=task.lower(),
data_per_task=True,
normalize_data=False,
t_min=times[0],
t_max=times[1],
read_events_from_file=False,
stim_channels='STI001',
use_empty_room_for_noise_cov=True,
n_jobs=args.n_jobs))
meg.call_main(args)
def calc_mne_python_sample_data(args):
import mne
mne_sample_data_fol = mne.datasets.sample.data_path()
trans_fname = op.join(mne_sample_data_fol, 'MEG', 'sample',
'sample_audvis_raw-trans.fif')
args = meg.read_cmd_args(
dict(
subject=args.subject,
mri_subject=args.mri_subject,
function='read_sensors_layout,calc_evokes',
# atlas='laus250',
contrast='audvis',
task='audvis',
trans_fname=trans_fname,
fname_format='{subject}_audvis-{ana_type}.{file_type}',
fname_format_cond='{subject}_audvis_{cond}-{ana_type}.{file_type}',
conditions=['LA', 'RA'],
read_events_from_file=True,
t_min=-0.2,
t_max=0.5,
extract_mode=['mean_flip'], #, 'mean', 'pca_flip'],
overwrite_epochs=args.overwrite,
overwrite_evoked=True,
overwrite_sensors=True))
meg.call_main(args)
def _calc_pvals_fMRI_clusters(p, extract_time_series_for_clusters=False):
subject, overwrite = p
stc_name = 'dSPM_mean_flip_vertices_power_spectrum_stat'
if not utils.both_hemi_files_exist(
op.join(MMVT_DIR, subject, 'meg', '{}-{}.stc'.format(
stc_name, '{hemi}'))):
print('{}: Can\'t find {}!'.format(subject, stc_name))
return False
args.subject = subject
clusters_root_fol = utils.make_dir(
op.join(MMVT_DIR, subject, 'meg', 'clusters'))
res_fname = op.join(
clusters_root_fol,
'clusters_labels_dSPM_mean_flip_vertices_power_spectrum_stat.pkl')
if not op.isfile(res_fname) or args.overwrite:
utils.delete_folder_files(clusters_root_fol)
_args = meg.read_cmd_args(
dict(subject=subject,
mri_subject=subject,
atlas='MSIT_I-C',
function='find_functional_rois_in_stc',
stc_name=stc_name,
threshold=-np.log10(0.01),
threshold_is_precentile=False,
extract_time_series_for_clusters=False,
save_func_labels=True,
calc_cluster_contours=True,
n_jobs=args.n_jobs))
try:
meg.call_main(_args)
except:
print(traceback.format_exc())
if not op.isfile(res_fname):
print('Cluster output can\'t be found!')
return False
def calc_msit(args):
# python -m src.preproc.meg -s ep001 -m mg78 -a laus250 -t MSIT
# --contrast interference --t_max 2 --t_min -0.5 --data_per_task 1 --read_events_from_file 1
# --events_fname {subject}_msit_nTSSS_interference-eve.txt --cleaning_method nTSSS
args = meg.read_cmd_args(dict(
subject=args.subject,
mri_subject=args.mri_subject,
task='MSIT',
# function=args.real_function,
function='read_sensors_layout,calc_epochs,calc_evokes,calc_stc,calc_labels_avg_per_condition,calc_labels_min_max',
data_per_task=True,
atlas=args.atlas,
contrast='interference',
cleaning_method='nTSSS',
t_min=-0.5,
t_max=2,
# calc_epochs_from_raw=True,
read_events_from_file=True,
# remote_subject_meg_dir='/autofs/space/sophia_002/users/DARPA-MEG/project_orig_msit',
events_fname='{subject}_msit_nTSSS_interference-eve.txt',
reject=False,
# save_smoothed_activity=True,
# stc_t=1189,
morph_to_subject = 'fsaverage5',
extract_mode=['mean_flip'], #, 'mean', 'pca_flip'],
pick_ori='normal',
overwrite_epochs=False,
overwrite_evoked=True,
overwrite_stc=False,
overwrite_labels_data=False,
overwrite_sensors=False
))
meg.call_main(args)
def calc_sample_meg_data():
args = meg.read_cmd_args(
dict(subject='sample',
function='calc_epochs,calc_evokes,calc_stc',
contrast='audvis',
task='audvis',
pick_meg=True,
pick_eeg=False,
fwd_usingMEG=True,
fwd_usingEEG=False,
fname_format='{subject}_audvis_meg-{ana_type}.{file_type}',
fname_format_cond=
'{subject}_audvis_meg_{cond}-{ana_type}.{file_type}',
trans_fname=op.join(MNE_ROOT, 'sample_audvis_raw-trans.fif'),
events_fname=op.join(MNE_ROOT, 'sample_audvis_raw-eve.fif'),
raw_fname=op.join(MNE_ROOT, 'sample_audvis_raw.fif'),
inv_fname=op.join(MNE_ROOT,
'sample_audvis-meg-oct-6-meg-inv.fif'),
fwd_fname=op.join(MNE_ROOT, 'sample_audvis-meg-oct-6-fwd.fif'),
conditions=['LA', 'RA'],
read_events_from_file=True,
t_min=-0.2,
t_max=0.5,
overwrite_epochs=False,
overwrite_evoked=False,
overwrite_stc=True))
meg.call_main(args)
def calc_fwd_inv(subject, raw_fname, empty_fname, bad_channels_fname, overwrite_inv=False,
overwrite_fwd=False):
# python -m src.preproc.eeg -s nmr00857 -f calc_inverse_operator,make_forward_solution
# --overwrite_inv 0 --overwrite_fwd 0 -t epilepsy
# --raw_fname /autofs/space/frieda_001/users/valia/epilepsy/5241495_00857/subj_5241495/190123/5241495_01_raw.fif
# --empty_fname /autofs/space/frieda_001/users/valia/epilepsy/5241495_00857/subj_5241495/190123/5241495_roomnoise_raw.fif
# --use_empty_room_for_noise_cov 1
# --bad_channels EEG061,EEG02,EEG042,MEG0112,MEG0113
bad_channels = ','.join(matlab_utils.matlab_cell_arrays_to_dict(bad_channels_fname)['label'])
trans_fname = op.join(MEG_DIR, subject, '{}-trans.fif'.format(subject))
args = meg.read_cmd_args(dict(
subject=subject,
mri_subject=subject,
function='calc_inverse_operator,make_forward_solution',
task='kaggle',
inv_fname=op.join(MEG_DIR, subject, '{}-meeg-kaggle-inv.fif'.format(subject)),
fwd_fname=op.join(MEG_DIR, subject, '{}-meeg-kaggle-fwd.fif'.format(subject)),
fwd_usingEEG=True,
overwrite_inv=overwrite_inv,
overwrite_fwd=overwrite_fwd,
use_empty_room_for_noise_cov=True,
bad_channels=bad_channels,
raw_fname=raw_fname,
empty_fname=empty_fname,
cor_fname=trans_fname
))
meg.call_main(args)
def calc_msit_functional_rois(args):
clusters_root_fol = utils.make_dir(
op.join(MMVT_DIR, args.subject[0], 'meg', 'clusters'))
utils.delete_folder_files(clusters_root_fol)
# conditions = ['neutral', 'interference']
# for cond in conditions:
_args = meg.read_cmd_args(
dict(
subject=args.subject,
mri_subject=args.mri_subject,
task='MSIT',
data_per_task=True,
# atlas='laus125',
function='find_functional_rois_in_stc',
inverse_method='dSPM',
stc_name=
'{subject}_msit_nTSSS_interference_interference-neutral_1-15-dSPM',
inv_fname='{subject}_msit_nTSSS_interference_1-15-inv',
label_name_template='*',
peak_mode='pos',
threshold=99.5,
min_cluster_max=5,
min_cluster_size=100,
# recreate_src_spacing='ico5'
# clusters_label='precentral'
))
meg.call_main(_args)
def calc_power_spectrum(args):
args = meg.read_cmd_args(dict(
subject=args.subject,
mri_subject=args.mri_subject,
atlas='laus125',
function='calc_power_spectrum',
overwrite_labels_power_spectrum=True,
task='rest',
))
meg.call_main(args)
def morph_stc(args):
args = meg.read_cmd_args(dict(
subject=args.subject,
mri_subject=args.mri_subject,
function='morph_stc',
task='MSIT',
data_per_task=True,
contrast='interference',
cleaning_method='nTSSS',
morph_to_subject='colin27'))
meg.call_main(args)
def calc_functional_rois(args):
# -s DC -a laus250 -f find_functional_rois_in_stc --stc_name right-MNE-1-15 --label_name_template "precentral*" --inv_fname right-inv --threshold 99.5
args = meg.read_cmd_args(
dict(subject=args.subject,
mri_subject=args.mri_subject,
atlas='laus125',
function='find_functional_rois_in_stc',
inverse_method='MNE',
stc_name='right-MNE-1-15',
label_name_template='precentral*',
inv_fname='right-inv',
threshold=99.5))
meg.call_main(args)
def calc_labels_connectivity(args):
args = meg.read_cmd_args(dict(
subject=args.subject,
mri_subject=args.mri_subject,
task='MSIT',
function='calc_labels_connectivity',
data_per_task=True,
# atlas='laus125',
contrast='interference',
cleaning_method='nTSSS',
pick_ori='normal',
con_method='wpli2_debiased'
))
meg.call_main(args)
def calc_mne_python_sample_data(args):
args = meg.read_cmd_args(
dict(
subject=args.subject,
mri_subject=args.mri_subject,
# atlas='laus250',
contrast='audvis',
fname_format='{subject}_audvis-{ana_type}.{file_type}',
fname_format_cond='{subject}_audvis_{cond}-{ana_type}.{file_type}',
conditions=['LA', 'RA'],
read_events_from_file=True,
t_min=-0.2,
t_max=0.5,
extract_mode=['mean_flip', 'mean', 'pca_flip']))
meg.call_main(args)
def meg_calc_labels_ts(subject, inv_method='MNE', em='mean_flip', atlas='electrodes_labels', remote_subject_dir='',
meg_remote_dir='', empty_fname='', cor_fname='', use_demi_events=True, n_jobs=-1):
functions = 'calc_epochs,calc_evokes,make_forward_solution,calc_inverse_operator,calc_stc,calc_labels_avg_per_condition'
meg_args = meg.read_cmd_args(dict(
subject=subject, mri_subject=subject,
task='rest', inverse_method=inv_method, extract_mode=em, atlas=atlas,
single_trial_stc=True,
recreate_src_spacing='ico5',
# fwd_recreate_source_space=True,
# recreate_bem_solution=True,
remote_subject_meg_dir=meg_remote_dir,
remote_subject_dir=remote_subject_dir,
empty_fname=empty_fname,
cor_fname=cor_fname,
function=functions,
use_demi_events=use_demi_events,
windows_length=10000,
windows_shift=5000,
# overwrite_fwd=True,
# overwrite_inv=True,
# overwrite_labels_data=True,
using_auto_reject=False,
use_empty_room_for_noise_cov=True,
read_only_from_annot=False,
n_jobs=n_jobs
))
return meg.call_main(meg_args)
def meg_preproc(subject, inv_method='MNE', em='mean_flip', atlas='electrodes_labels', remote_subject_dir='',
meg_remote_dir='', empty_fname='', cor_fname='', use_demi_events=True, calc_labels_avg=False,
overwrite=False, n_jobs=-1):
functions = 'calc_epochs,calc_evokes,make_forward_solution,calc_inverse_operator'
if calc_labels_avg:
functions += ',calc_stc,calc_labels_avg_per_condition'
meg_args = meg.read_cmd_args(dict(
subject=subject, mri_subject=subject,
task='rest', inverse_method=inv_method, extract_mode=em, atlas=atlas,
remote_subject_meg_dir=meg_remote_dir,
remote_subject_dir=remote_subject_dir,
empty_fname=empty_fname,
cor_fname=cor_fname,
function=functions,
use_demi_events=use_demi_events,
windows_length=10000,
windows_shift=5000,
# power_line_notch_widths=5,
using_auto_reject=False,
# reject=False,
use_empty_room_for_noise_cov=True,
read_only_from_annot=False,
overwrite_epochs=overwrite,
overwrite_evoked=overwrite,
n_jobs=n_jobs
))
return meg.call_main(meg_args)
def meg_preproc(args):
atlas, inv_method, em = 'aparc.DKTatlas40', 'dSPM', 'mean_flip'
atlas = 'darpa_atlas'
bands = dict(theta=[4, 8], alpha=[8, 15], beta=[15, 30], gamma=[30, 55], high_gamma=[65, 200])
tasks = ['MSIT', 'ECR']
empty_fnames = get_empty_fnames(args.subject[0], tasks, args)
times = (-2, 4)
for task in tasks:
args = meg.read_cmd_args(dict(
subject=args.subject, mri_subject=args.subject,
task=task, inverse_method=inv_method, extract_mode=em, atlas=atlas,
meg_dir=args.meg_dir,
remote_subject_dir=args.remote_subject_dir, # Needed for finding COR
get_task_defaults=False,
fname_format='{}_{}_maxwell-raw'.format('{subject}', task),
empty_fname=empty_fnames[task],
# function='calc_epochs,calc_evokes,make_forward_solution,calc_inverse_operator,calc_stc_per_condition,calc_labels_avg_per_condition,calc_labels_min_max',
function='calc_epochs',
# function='calc_labels_connectivity',
conditions=task.lower(),
# data_per_task=True,
ica_overwrite_raw=False,
normalize_data=False,
t_min=times[0], t_max=times[1],
read_events_from_file=False, stim_channels='STI001',
use_empty_room_for_noise_cov=True,
calc_source_band_induced_power=True,
calc_inducde_power_per_label=False,
bands='', #dict(theta=[4, 8], alpha=[8, 15], beta=[15, 30], gamma=[30, 55], high_gamma=[65, 200]),
con_method='coh',
con_mode='cwt_morlet',
overwrite_connectivity=False,
read_only_from_annot=False,
# pick_ori='normal',
# overwrite_epochs=True,
# overwrite_evoked=True,
# overwrite_inv=True,
overwrite_stc=True,
overwrite_labels_data=True,
n_jobs=args.n_jobs
))
meg.call_main(args)
#
for subject in args.subject:
for task in tasks:
task = task.lower()
def meg_remove_artifcats(subject, raw_fname):
meg_args = meg.read_cmd_args(dict(
subject=subject, mri_subject=subject,
function='remove_artifacts',
raw_fname=raw_fname,
overwrite_ica=True
))
return meg.call_main(meg_args)
def calc_fwd_inv(subject, raw_fname, bad_channels, empty_room_fname,
remote_subject_dir, fwd_usingMEG, fwd_usingEEG, overwrite,
n_jobs):
args = meg.read_cmd_args(
dict(subject=subject,
task='epilepsy',
function='make_forward_solution,calc_inverse_operator',
raw_fname=raw_fname,
bad_channels=bad_channels,
use_empty_room_for_noise_cov=True,
empty_fname=empty_room_fname,
fwd_usingMEG=fwd_usingMEG,
fwd_usingEEG=fwd_usingEEG,
remote_subject_dir=remote_subject_dir,
overwrite_fwd=overwrite,
overwrite_inv=overwrite,
n_jobs=n_jobs))
meg.call_main(args)
def calc_msit_labels_avg(args):
# python -m src.preproc.meg -s ep001 -m mg78 -a laus250 -t MSIT
# --contrast interference --t_max 2 --t_min -0.5 --data_per_task 1 --read_events_from_file 1
# --events_fname {subject}_msit_nTSSS_interference-eve.txt --cleaning_method nTSSS
args = meg.read_cmd_args(
dict(subject=args.subject,
mri_subject=args.mri_subject,
task='MSIT',
function='calc_labels_avg_per_condition,calc_labels_min_max',
data_per_task=True,
atlas=args.atlas,
contrast='interference',
cleaning_method='nTSSS',
t_min=-0.5,
t_max=2,
pick_ori='normal',
overwrite_labels_data=True))
meg.call_main(args)
def read_meg_layouts(_args, remote_raw_fname=''):
args = copy.copy(_args)
bad_subjects = []
output_fol = utils.make_dir(op.join(MMVT_DIR, 'sensors'))
subjects = args.subject
for subject in subjects:
args.subject = [subject]
_, _, trans_fname = get_meg_empty_fnames(subject, args.remote_meg_dir,
args)
if remote_raw_fname == '':
remote_raw_fname = op.join(
args.raw_rest_remote_fol, subject,
'{}_Resting_meg_ica-raw.fif'.format(subject))
if not op.isfile(remote_raw_fname):
print('No Cor fname: {}!!!'.format(remote_raw_fname))
continue
meg_args = meg.read_cmd_args(
utils.Bag(subject=subject,
data_per_task=False,
remote_subject_dir=args.remote_subject_dir,
raw_fname=remote_raw_fname,
function='read_sensors_layout',
trans_fname=trans_fname,
overwrite_sensors=True,
read_info_file=False,
n_jobs=args.n_jobs))
meg.call_main(meg_args)
for sensor_type in ['mag', 'planar1', 'planar2']:
sensors_fname = op.join(
MMVT_DIR, subject, 'meg',
'meg_{}_sensors_positions.npz'.format(sensor_type))
if not op.isfile(sensors_fname):
bad_subjects.append(subject)
break
utils.make_dir(op.join(output_fol, subject))
output_fname = op.join(output_fol, subject,
utils.namebase_with_ext(sensors_fname))
if not op.isfile(output_fname):
utils.copy_file(sensors_fname, output_fname)
print('{}/{} subjects with no sensors:'.format(len(bad_subjects),
len(args.subject)))
print(bad_subjects)
def calc_meg_power_spectrum(subject, atlas, inv_method, em, overwrite=False, n_jobs=-1):
meg_args = meg.read_cmd_args(dict(
subject=subject, mri_subject=subject,
task='rest', inverse_method=inv_method, extract_mode=em, atlas=atlas,
function='calc_labels_power_spectrum',
pick_ori='normal', # very important for calculation of the power spectrum
# max_epochs_num=20,
overwrite_labels_power_spectrum=overwrite,
n_jobs=n_jobs
))
return meg.call_main(meg_args)
def mmvt():
from src.preproc import meg
# Call the MMVT MEG preprocessing to create the inverse solution and the source estimate
args = meg.read_cmd_args(
dict(subject='sample',
task='audvis',
inverse_method='MNE',
pick_ori=None,
function='calc_inverse_operator,calc_stc',
inv_loose=0,
evo_fname=fname_evoked,
fwd_fname=fname_fwd,
noise_cov_fname=fname_cov))
meg.call_main(args)
stc_fname = meg.get_stc_fname(args).format(hemi='lh')
t = meg.time_to_index(0.08)
stc_fname, _ = mmvt.meg.plot_stc(stc_fname,
t=168,
threshold=1.43,
save_image=True)
def calc_functional_rois(conds, args):
clusters_root_fol = op.join(MMVT_DIR, subject, 'meg', 'clusters')
utils.delete_folder_files(clusters_root_fol)
for cond in conds.keys():
_args = meg.read_cmd_args(
dict(
subject=args.subject,
mri_subject=args.mri_subject,
atlas='laus250',
function='find_functional_rois_in_stc',
inverse_method='MNE',
stc_name='{}-MNE-1-15'.format(cond),
label_name_template='precentral*',
inv_fname='{}-inv'.format(cond),
threshold=99.5,
min_cluster_max=0.2,
min_cluster_size=100,
# clusters_label='precentral'
))
meg.call_main(_args)
def calc_msit_evoked(args):
# python -m src.preproc.meg -s ep001 -m mg78 -a laus125 -f calc_epochs,calc_evokes -t MSIT
# --contrast interference --t_max 2 --t_min -0.5 --data_per_task 1 --read_events_from_file 1
# --events_fname {subject}_msit_nTSSS_interference-eve.txt --cleaning_method nTSSS
args = meg.read_cmd_args(dict(
subject=args.subject,
mri_subject=args.mri_subject,
task='MSIT',
function='calc_epochs,calc_evokes',
data_per_task=True,
atlas='laus125',
contrast='interference',
cleaning_method='nTSSS',
t_min=-0.5,
t_max=2,
read_events_from_file=True,
normalize_data = False,
overwrite_evoked = True,
events_fname='{subject}_msit_nTSSS_interference-eve.txt',
))
meg.call_main(args)
def main(subject,
atlas,
connectivity_method,
graph_func,
remote_subject_dir,
files,
n_jobs=4):
meg_fol = op.join(MMVT_DIR, subject, 'meg')
for fname in files:
file_name = utils.namebase(fname)
files_fol = utils.make_dir(op.join(meg_fol, file_name))
files_exist = \
utils.both_hemi_files_exist(op.join(files_fol, '{}_all-dSPM-{}.stc'.format(subject, '{hemi}'))) and \
utils.both_hemi_files_exist(op.join(files_fol, 'labels_data_epilepsy_laus125_dSPM_mean_flip_{hemi}.npz'))
if not files_exist:
args = meg.read_cmd_args(
dict(subject=subject,
task='epilepsy',
function='calc_stc,calc_labels_avg_per_condition',
atlas=atlas,
evo_fname=fname,
remote_subject_dir=remote_subject_dir,
overwrite_labels_data=True,
n_jobs=n_jobs))
meg.call_main(args)
analyse_connectivity(subject, connectivity_method, graph_func,
file_name, atlas, n_jobs)
for hemi in utils.HEMIS:
utils.move_file(
op.join(meg_fol, '{}_all-dSPM-{}.stc'.format(subject, hemi)),
files_fol)
utils.move_file(
op.join(
meg_fol,
'labels_data_epilepsy_laus125_dSPM_mean_flip_{}.npz'.
format(hemi)), files_fol)
plot_all_files_graph_max(subject, files, graph_func)
def analyze_meg(args):
subjects = args.subject
for subject, mri_subject in zip(subjects, args.mri_subject):
init_meg(subject)
local_rest_raw_fname, empty_fname, cor_fname = get_meg_empty_fnames(
subject, args.remote_meg_dir.format(subject=subject.upper()), args)
if not op.isfile(empty_fname) or not op.isfile(cor_fname):
print('{}: Can\'t find empty, raw, or cor files!'.format(subject))
continue
args = meg.read_cmd_args(
dict(
subject=subject,
mri_subject=mri_subject,
atlas=args.atlas,
function='rest_functions',
task='rest',
reject=
True, # Should be True here, unless you are dealling with bad data...
remove_power_line_noise=True,
l_freq=3,
h_freq=80,
windows_length=500,
windows_shift=100,
inverse_method='MNE',
raw_fname=local_rest_raw_fname,
cor_fname=cor_fname,
empty_fname=empty_fname,
remote_subject_dir=args.remote_subject_dir,
# This properties are set automatically if task=='rest'
# calc_epochs_from_raw=True,
# single_trial_stc=True,
# use_empty_room_for_noise_cov=True,
# windows_num=10,
# baseline_min=0,
# baseline_max=0,
))
meg.call_main(args)
def meg_prepoc(args):
# -s nmr00479 -f make_forward_solution,calc_inverse_operator,calc_stc --use_empty_room_for_noise_cov 1 --apply_on_raw 1 --recreate_src_surface 1 --overwrite_fwd 1
inv_method = 'MNE'
for subject in args.subject:
raw_files = glob.glob(op.join(MEG_DIR, subject, '*_??_raw.fif'))
args.subject = subject
for raw_fname in raw_files:
meg_args = meg.read_cmd_args(dict(
subject=args.subject, mri_subject=args.subject,
inverse_method=inv_method,
raw_fname=raw_fname,
function='make_forward_solution,calc_inverse_operator,calc_stc',
use_empty_room_for_noise_cov=True,
apply_on_raw=True,
pick_ori='normal'
))
ret = meg.call_main(meg_args)
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 calc_meg_source_psd(args):
from src.misc import meg_buddy
bad_subjects = ['hc004', 'hc012', 'hc029']
subjects = args.subject
for subject in subjects:
if subject in bad_subjects:
continue
fol = op.join(MMVT_DIR, subject, 'meg')
file_name = '{cond}_dSPM_mean_flip_vertices_power_spectrum.pkl'
if all([op.isfile(op.join(fol, file_name.format(cond=cond.lower())))
for cond in MSIT_CONDS]) and not args.overwrite:
print('{}: already has MSIT power stcs'.format(subject))
continue
args.subject = subject
local_raw_fname = op.join(MEG_DIR, args.task, subject, args.raw_template.format(
subject=subject, task=args.task))
remote_raw_fname = op.join(args.remote_root_dir, 'raw_preprocessed', subject, args.raw_template.format(
subject=subject, task=args.task))
if not op.isfile(remote_raw_fname) and not args.ignore:
print('Can\'t find remote raw file! {}'.format(remote_raw_fname))
continue
if op.isfile(local_raw_fname):
os.remove(local_raw_fname)
utils.make_link(remote_raw_fname, local_raw_fname)
if not op.islink(local_raw_fname) and not args.ignore:
print('Can\'t create a link to the remote raw!')
continue
inv_fname = op.join(MEG_DIR, args.task, subject, args.inv_template.format(subject=subject, task=args.task))
if not op.isfile(inv_fname):
inv_fnames = glob.glob(op.join(MEG_DIR, args.task, subject, '*inv.fif'))
if len(inv_fnames) > 0:
inv_fname = utils.select_one_file(inv_fnames)
print('New inv fname: {}'.format(inv_fname))
_args = meg.read_cmd_args(dict(
subject=subject, mri_subject=subject,
function='make_forward_solution,calc_inverse_operator',
task='MSIT', data_per_task=True,
fmin=1, fmax=120,
raw_fname=local_raw_fname, inv_fname=inv_fname,
remote_subject_dir=args.remote_subject_dir,
n_jobs=args.n_jobs
))
ret = meg.call_main(_args)
if not ret[subject].get('calc_inverse_operator', True):
continue
# Load the eopchs and calc source power spectrum for both conditions.
# The epochs are being splitted first
data = meg_buddy.get_data(subject, tasks=['MSIT'], modalities=['MEG'])['MSIT']['MEG']
if subject not in data:
print('{} not in msit_data!'.format(subject))
continue
data = data[subject]
subject_epochs = data._load_epochs('Onset', ar=True)
indices = data._get_indices(subject_epochs, 'Condition', MSIT_CONDS)
for cond in MSIT_CONDS:
epochs = subject_epochs[indices[cond]]
meg.calc_source_power_spectrum(
subject, cond.lower(), epochs=epochs, max_epochs_num=50, inv_fname=inv_fname,
overwrite=args.overwrite, n_jobs=args.n_jobs)