def calc_labels_center_of_mass(subject, atlas, read_from_annotation=True, surf_name='pial', labels_fol='', labels=None):
import csv
# if (read_from_annotation):
# labels = mne.read_labels_from_annot(subject, atlas, 'both', surf_name, subjects_dir=SUBJECTS_DIR)
# if len(labels) == 0:
# print('No labels were found in {} annotation file!'.format(atlas))
# else:
# labels = []
# if labels_fol == '':
# labels_fol = op.join(SUBJECTS_DIR, subject, 'label', atlas)
# for label_file in glob.glob(op.join(labels_fol, '*.label')):
# label = mne.read_label(label_file)
# labels.append(label)
# if len(labels) == 0:
# print('No labels were found in {}!'.format(labels_fol))
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas)
if len(labels) > 0:
center_of_mass = lu.calc_center_of_mass(labels)
with open(op.join(SUBJECTS_DIR, subject, 'label', '{}_center_of_mass.csv'.format(atlas)), 'w') as csvfile:
writer = csv.writer(csvfile, delimiter=',')
for label in labels:
writer.writerow([label.name, *center_of_mass[label.name]])
com_fname = op.join(SUBJECTS_DIR, subject, 'label', '{}_center_of_mass.pkl'.format(atlas))
blend_fname = op.join(MMVT_DIR, subject, '{}_center_of_mass.pkl'.format(atlas))
utils.save(center_of_mass, com_fname)
shutil.copyfile(com_fname, blend_fname)
return len(labels) > 0 and op.isfile(com_fname) and op.isfile(blend_fname)
def save_labels_coloring(subject, atlas, n_jobs=2):
ret = False
coloring_dir = op.join(MMVT_DIR, subject, 'coloring')
utils.make_dir(coloring_dir)
coloring_fname = op.join(coloring_dir, 'labels_{}_coloring.csv'.format(atlas))
coloring_names_fname = op.join(coloring_dir, 'labels_{}_colors_names.csv'.format(atlas))
try:
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas, n_jobs=n_jobs)
colors_rgb_and_names = cu.get_distinct_colors_and_names()
labels_colors_rgb, labels_colors_names = {}, {}
for label in labels:
label_inv_name = lu.get_label_hemi_invariant_name(label.name)
if label_inv_name not in labels_colors_rgb:
labels_colors_rgb[label_inv_name], labels_colors_names[label_inv_name] = next(colors_rgb_and_names)
with open(coloring_fname, 'w') as colors_file, open(coloring_names_fname, 'w') as col_names_file:
for label in labels:
label_inv_name = lu.get_label_hemi_invariant_name(label.name)
color_rgb = labels_colors_rgb[label_inv_name]
color_name = labels_colors_names[label_inv_name]
colors_file.write('{},{},{},{}\n'.format(label.name, *color_rgb))
col_names_file.write('{},{}\n'.format(label.name, color_name))
ret = op.isfile(coloring_fname)
except:
print('Error in save_labels_coloring!')
print(traceback.format_exc())
return ret
def init(subject, atlas, n_jobs):
from src.utils import geometry_utils as gu
if not utils.both_hemi_files_exist(
op.join(SUBJECTS_DIR, subject, 'label', '{}.{}.annot'.format(
'{hemi}', atlas))):
anat.create_annotation(subject, atlas)
if not utils.both_hemi_files_exist(
op.join(SUBJECTS_DIR, subject, 'label', '{}.{}.annot'.format(
'{hemi}', atlas))):
raise Exception(
'Can\'t find the cortical atlas {} for subject {}'.format(
atlas, subject))
labels_vertices = find_rois.read_labels_vertices(SUBJECTS_DIR, subject,
atlas, n_jobs)
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas)
labels_names = [l.name for l in labels]
aseg_atlas_fname = op.join(SUBJECTS_DIR, subject, 'mri', 'aseg.mgz')
aseg_data = nib.load(aseg_atlas_fname).get_data()
lut = fu.import_freesurfer_lut()
pia_verts = {}
for hemi in ['rh', 'lh']:
pia_verts[hemi], _ = gu.read_surface(
op.join(SUBJECTS_DIR, subject, 'surf', '{}.pial'.format(hemi)))
# pia_verts[hemi], _ = nib.freesurfer.read_geometry(
# op.join(SUBJECTS_DIR, subject, 'surf', '{}.pial'.format(hemi)))
subs_center_of_mass, subs_names = calc_subcorticals_pos(
subject, aseg_data, lut)
labels_center_of_mass = lu.calc_center_of_mass(labels, ret_mat=True) * 1000
regions_center_of_mass = np.concatenate(
(labels_center_of_mass, subs_center_of_mass))
regions_names = labels_names + subs_names
# save_com_as_elecs(subject, regions_center_of_mass, regions_names, atlas)
# save_com_as_elecs(subject, subs_center_of_mass, subs_names, atlas)
return labels_vertices, regions_center_of_mass, regions_names, aseg_data, lut, pia_verts,
def save_rois_connectivity(subject, args):
# atlas, mat_fname, mat_field, conditions, stat=STAT_DIFF, windows=0,
# labels_exclude=['unknown', 'corpuscallosum'], threshold=0, threshold_percentile=0,
# color_map='jet', norm_by_percentile=True, norm_percs=(1, 99), symetric_colors=True):
# args.atlas, args.mat_fname, args.mat_field, args.conditions, args.stat,
# args.windows, args.labels_exclude, args.threshold, args.threshold_percentile,
# args.color_map, args.norm_by_percentile, args.norm_percs)
d = dict()
data = sio.loadmat(args.mat_fname)[args.mat_field]
d['labels'] = lu.read_labels(subject,
SUBJECTS_DIR,
args.atlas,
exclude=args.labels_exclude,
sorted_according_to_annot_file=True)
d['locations'] = lu.calc_center_of_mass(d['labels'], ret_mat=True) * 1000
d['hemis'] = ['rh' if l.hemi == 'rh' else 'lh' for l in d['labels']]
d['labels'] = [l.name for l in d['labels']]
(d['con_colors'], d['con_indices'], d['con_names'], d['con_values'],
d['con_types'], d['data_max'],
d['data_min']) = calc_connections_colors(data, d['labels'], d['hemis'],
args)
# args.stat, args.conditions, args.windows, args.threshold,
# args.threshold_percentile, args.color_map, args.norm_by_percentile, args.norm_percs, args.symetric_colors)
d['conditions'] = args.conditions
np.savez(op.join(BLENDER_ROOT_DIR, subject, 'rois_con'), **d)
def calc_rois_connectivity(
subject, clips, modality, atlas, inverse_method, min_order=1, max_order=20, crop_times=(-0.5, 1),
onset_time=2, windows_length=0.1, windows_shift=0.05, overwrite=False, n_jobs=4):
windows_length *= 1000
windows_shift *= 1000
params = []
clusters_fol = op.join(MMVT_DIR, subject, meg.modality_fol(modality), 'clusters')
fwd_usingMEG, fwd_usingEEG = meg.get_fwd_flags(modality)
bands = {'all': [None, None]}
crop_times = [t + onset_time for t in crop_times]
use_functional_rois_atlas = False
conds = [utils.namebase(clip_fname) for clip_fname in clips['ictal']]
conds.extend(['{}_baseline'.format(utils.namebase(clip_fname)) for clip_fname in clips['baseline']])
if not use_functional_rois_atlas:
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas)
func_atlas = con_indentifer = atlas
for clip_fname, cond in zip(clips['ictal'] + clips['baseline'], conds):
if use_functional_rois_atlas:
check_connectivity_labels(clips['ictal'], modality, inverse_method, n_jobs=n_jobs)
labels_fol = op.join(
clusters_fol, '{}-epilepsy-{}-{}-{}-amplitude-zvals'.format(
subject, inverse_method, modality, utils.namebase(clip_fname)))
labels = lu.read_labels_files(subject, labels_fol, n_jobs=n_jobs)
# for connectivity we need shorter names
labels = epi_utils.shorten_labels_names(labels)
func_atlas = utils.namebase(clip_fname)
con_indentifer = 'func_rois'
params.append((
subject, clip_fname, utils.namebase(clip_fname), func_atlas, labels, inverse_method, fwd_usingMEG,
fwd_usingEEG, crop_times, bands, min_order, max_order, windows_length, windows_shift, con_indentifer,
overwrite, 1))
utils.run_parallel(_calc_clip_rois_connectivity_parallel, params, n_jobs)
def calc_labels_center_of_mass(subject, atlas, read_from_annotation=True, surf_name='pial', labels_fol='', labels=None):
import csv
# if (read_from_annotation):
# labels = mne.read_labels_from_annot(subject, atlas, 'both', surf_name, subjects_dir=SUBJECTS_DIR)
# if len(labels) == 0:
# print('No labels were found in {} annotation file!'.format(atlas))
# else:
# labels = []
# if labels_fol == '':
# labels_fol = op.join(SUBJECTS_DIR, subject, 'label', atlas)
# for label_file in glob.glob(op.join(labels_fol, '*.label')):
# label = mne.read_label(label_file)
# labels.append(label)
# if len(labels) == 0:
# print('No labels were found in {}!'.format(labels_fol))
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas)
if len(labels) > 0:
center_of_mass = lu.calc_center_of_mass(labels)
with open(op.join(SUBJECTS_DIR, subject, 'label', '{}_center_of_mass.csv'.format(atlas)), 'w') as csvfile:
writer = csv.writer(csvfile, delimiter=',')
for label in labels:
writer.writerow([label.name, *center_of_mass[label.name]])
com_fname = op.join(SUBJECTS_DIR, subject, 'label', '{}_center_of_mass.pkl'.format(atlas))
blend_fname = op.join(MMVT_DIR, subject, '{}_center_of_mass.pkl'.format(atlas))
utils.save(center_of_mass, com_fname)
shutil.copyfile(com_fname, blend_fname)
return len(labels) > 0 and op.isfile(com_fname) and op.isfile(blend_fname)
def save_labels_coloring(subject, atlas, n_jobs=2):
ret = False
coloring_dir = op.join(MMVT_DIR, subject, 'coloring')
utils.make_dir(coloring_dir)
coloring_fname = op.join(coloring_dir, 'labels_{}_coloring.csv'.format(atlas))
coloring_names_fname = op.join(coloring_dir, 'labels_{}_colors_names.csv'.format(atlas))
try:
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas, n_jobs=n_jobs)
colors_rgb_and_names = cu.get_distinct_colors_and_names()
labels_colors_rgb, labels_colors_names = {}, {}
for label in labels:
label_inv_name = lu.get_label_hemi_invariant_name(label.name)
if label_inv_name not in labels_colors_rgb:
labels_colors_rgb[label_inv_name], labels_colors_names[label_inv_name] = next(colors_rgb_and_names)
with open(coloring_fname, 'w') as colors_file, open(coloring_names_fname, 'w') as col_names_file:
for label in labels:
label_inv_name = lu.get_label_hemi_invariant_name(label.name)
color_rgb = labels_colors_rgb[label_inv_name]
color_name = labels_colors_names[label_inv_name]
colors_file.write('{},{},{},{}\n'.format(label.name, *color_rgb))
col_names_file.write('{},{}\n'.format(label.name, color_name))
ret = op.isfile(coloring_fname)
except:
print('Error in save_labels_coloring!')
print(traceback.format_exc())
return ret
def calc_dipoles_rois(subject, atlas='laus125', overwrite=False, n_jobs=4):
links_dir = utils.get_links_dir()
subjects_dir = utils.get_link_dir(links_dir, 'subjects')
mmvt_dir = utils.get_link_dir(links_dir, 'mmvt')
diploes_rois_output_fname = op.join(mmvt_dir, subject, 'meg', 'dipoles_rois.pkl')
if op.isfile(diploes_rois_output_fname) and not overwrite:
diploes_rois = utils.load(diploes_rois_output_fname)
for dip in diploes_rois.keys():
diploes_rois[dip]['cortical_probs'] *= 1/sum(diploes_rois[dip]['cortical_probs'])
diploes_rois[dip]['subcortical_probs'] = []
diploes_rois[dip]['subcortical_rois'] = []
# coritcal_labels = set(utils.flat_list_of_lists([diploes_rois[k]['cortical_rois'] for k in diploes_rois.keys()]))
utils.save(diploes_rois, diploes_rois_output_fname)
return True
diploes_input_fname = op.join(mmvt_dir, subject, 'meg', 'dipoles.pkl')
if not op.isfile(diploes_input_fname):
print('No dipoles file!')
return False
labels = lu.read_labels(subject, subjects_dir, atlas, n_jobs=n_jobs)
labels = list([{'name': label.name, 'hemi': label.hemi, 'vertices': label.vertices}
for label in labels])
if len(labels) == 0:
print('Can\'t find the labels for atlas {}!'.format(atlas))
return False
# find the find_rois package
mmvt_code_fol = utils.get_mmvt_code_root()
ela_code_fol = op.join(utils.get_parent_fol(mmvt_code_fol), 'electrodes_rois')
if not op.isdir(ela_code_fol) or not op.isfile(op.join(ela_code_fol, 'find_rois', 'main.py')):
print("Can't find ELA folder!")
print('git pull https://github.com/pelednoam/electrodes_rois.git')
return False
# load the find_rois package
try:
import sys
if ela_code_fol not in sys.path:
sys.path.append(ela_code_fol)
from find_rois import main as ela
except:
print('Can\'t load find_rois package!')
utils.print_last_error_line()
return False
dipoles_dict = utils.load(diploes_input_fname)
diploles_names, dipoles_pos = [], []
for cluster_name, dipoles in dipoles_dict.items():
for begin_t, _, x, y, z, _, _, _, _, _ in dipoles:
dipole_name = '{}_{}'.format(cluster_name, begin_t) if len(dipoles) > 1 else cluster_name
diploles_names.append(dipole_name.replace(' ', ''))
dipoles_pos.append([k * 1e3 for k in [x, y, z]])
dipoles_rois = ela.identify_roi_from_atlas(
atlas, labels, diploles_names, dipoles_pos, approx=3, elc_length=0, hit_only_cortex=True,
subjects_dir=subjects_dir, subject=subject, n_jobs=n_jobs)
# Convert the list to a dict
dipoles_rois_dict = {dipoles_rois['name']: dipoles_rois for dipoles_rois in dipoles_rois}
utils.save(dipoles_rois_dict, diploes_rois_output_fname)
def save_connectivity_to_blender(subject, atlas, data, conditions, stat, w=0, threshold=0, threshold_percentile=0):
d = {}
d['labels'] = lu.read_labels(subject, SUBJECTS_DIR, atlas, exclude=['unknown', 'corpuscallosum'],
sorted_according_to_annot_file=True)
d['locations'] = lu.calc_center_of_mass(d['labels'], ret_mat=True)
d['hemis'] = ['rh' if l.hemi == 'rh' else 'lh' for l in d['labels']]
d['labels'] = [l.name for l in d['labels']]
d['con_colors'], d['con_indices'], d['con_names'], d['con_values'], d['con_types'] = \
calc_connections_colors(data, d['labels'], d['hemis'], stat, w, threshold_percentile=threshold_percentile)
d['conditions'] = conditions
np.savez(op.join(BLENDER_ROOT_DIR, subject, 'rois_con'), **d)
def save_connectivity_to_blender(subject, atlas, data, conditions, stat, w=0, threshold=0, threshold_percentile=0):
d = {}
d['labels'] = lu.read_labels(subject, SUBJECTS_DIR, atlas, exclude=('unknown', 'corpuscallosum'),
sorted_according_to_annot_file=True)
d['locations'] = lu.calc_center_of_mass(d['labels'], ret_mat=True)
d['hemis'] = ['rh' if l.hemi == 'rh' else 'lh' for l in d['labels']]
d['labels'] = [l.name for l in d['labels']]
d['con_colors'], d['con_indices'], d['con_names'], d['con_values'], d['con_types'] = \
calc_connections_colors(data, d['labels'], d['hemis'], stat, w, threshold_percentile=threshold_percentile)
d['conditions'] = conditions
np.savez(op.join(BLENDER_ROOT_DIR, subject, 'rois_con'), **d)
def merge_fmri_connectivity(args):
con_method = 'corr'
threshold_perc = 90
template_con = utils.make_dir(
op.join(MMVT_DIR, args.template_brain, 'connectivity'))
output_fname = op.join(template_con, 'rest_{}.npz'.format(con_method))
output_mean_fname = op.join(template_con,
'rest_{}_mean.npz'.format(con_method))
if op.isfile(output_fname) and not args.overwrite:
print('Averaged connectivity already exist')
return True
tempalte_labels = lu.read_labels(args.template_brain, SUBJECTS_DIR,
args.atlas)
tempalte_labels = [
l for l in tempalte_labels
if lu.get_label_hemi_invariant_name(l) not in args.labels_exclude
]
all_con = None
subjects_num = 0
good_subjects = []
for subject in args.subject:
fmri_con_fname = op.join(MMVT_DIR, subject, 'connectivity',
'fmri_{}.npy'.format(con_method))
if not op.isfile(fmri_con_fname):
print('{} is missing!'.format(fmri_con_fname))
continue
subject_con = np.load(fmri_con_fname)
print('{}: con.shape {}'.format(subject, subject_con.shape))
if subject_con.shape[0] != len(tempalte_labels):
print('Wrong number of cortical labels!')
continue
print(np.min(subject_con), np.max(subject_con))
if all_con is None:
all_con = np.zeros(subject_con.shape)
all_con += subject_con
subjects_num += 1
good_subjects.append(subject)
all_con /= subjects_num
for w in all_con.shape[2]:
all_con[:, :, w] = sym_mat(all_con[:, :, w])
np.savez(output_fname,
con=all_con,
names=[l.name for l in tempalte_labels])
threshold = np.percentile(all_con, threshold_perc)
np.savez(output_mean_fname,
con=all_con.mean(axis=2),
threshold=threshold,
labels=[l.name for l in tempalte_labels])
print('Good subjects: {}'.format(good_subjects))
def check_labels():
from src.utils import labels_utils as lu
labels = np.load(op.join(root_path, 'labels_names.npy'))
labels = lu.read_labels('fsaverage',
SUBJECTS_DIR,
'laus125',
only_names=True,
sorted_according_to_annot_file=True)
# labels = np.array(labels)
print([(ind, l) for ind, l in enumerate(labels) if l.startswith('unk')])
print([(ind, l) for ind, l in enumerate(labels) if l.startswith('corp')])
remove_ids = np.array([1, 5, 114, 118]) - 1
print('asdf')
def pre_processing(subject, modality, atlas, empty_fname, overwrite=False, n_jobs=4):
# 0.0) calc fwd inv
calc_fwd_inv(subject, run_num, modality, raw_fname, empty_fname, bad_channels, overwrite, n_jobs)
# 0.1) If there is a problem with smoothing the surfaces, you should delete the morphing maps first
# delete_morphing_maps(subject)
# 0.2) Finds the trans file
trans_file = meg.find_trans_file(subject=subject)
# 0.3) Make sure we have a morph map, and if not, create it here, and not in the parallel function
mne.surface.read_morph_map(subject, subject, subjects_dir=SUBJECTS_DIR)
# 0.4) Make sure the label exist, if not, create them
anat.create_annotation(subject, atlas, n_jobs=n_jobs)
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas, n_jobs=n_jobs)
if len(labels) == 0:
raise Exception('No {} labels!'.format(atlas))
def find_vertices(subject, run_num, modality='meg', atlas='aparc.DKTatlas'):
from src.utils import labels_utils as lu
root_dir = op.join(EEG_DIR if modality == 'eeg' else MEG_DIR, subject)
inv_fname = op.join(
root_dir, '{}-epilepsy{}-{}-inv.fif'.format(subject, run_num,
modality))
inv = mne.minimum_norm.read_inverse_operator(inv_fname)
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas)
vertices = []
for ind, label in enumerate(labels):
_, vertno = mne.minimum_norm.inverse.label_src_vertno_sel(
label, inv['src'])
vertices.extend(vertno)
np.save(op.join(MMVT_DIR, subject, 'labels_verts.npy'), np.array(vertices))
return vertices
def calc_distances_from_rois(subject, dist_threshold=0.05):
from scipy.spatial.distance import cdist
import nibabel as nib
dipoles_dict = utils.load(op.join(MMVT_DIR, subject, 'meg', 'dipoles.pkl'))
labels_times_fol = op.join(MMVT_DIR, subject, 'meg', 'time_accumulate')
labels = lu.read_labels(subject, SUBJECTS_DIR, 'laus125')
labels_center_of_mass = lu.calc_center_of_mass(labels)
labels_pos = np.array([labels_center_of_mass[l.name] for l in labels])
labels_dict = {l.name: labels_center_of_mass[l.name] for l in labels}
outer_skin_surf_fname = op.join(SUBJECTS_DIR, subject, 'surf', 'lh.seghead')
outer_skin_surf_verts, _ = nib.freesurfer.read_geometry(outer_skin_surf_fname)
for dipole_name, dipoles in dipoles_dict.items():
dipole_pos = np.array([dipoles[0][2], dipoles[0][3], dipoles[0][4]])
lables_times_fname = op.join(labels_times_fol, '{}_labels_times.txt'.format(dipole_name))
if not op.isfile(lables_times_fname):
print('Can\'t find {}!'.format(lables_times_fname))
continue
dists_from_outer_skin = np.min(cdist(outer_skin_surf_verts * 0.001, [dipole_pos]), 0)[0]
output_fname = op.join(labels_times_fol, '{}_labels_times_dists.txt'.format(dipole_name))
lines = utils.csv_file_reader(lables_times_fname, delimiter=':', skip_header=1)
output, dists = [], []
labels_dists = cdist(labels_pos, [dipole_pos])
dists_argmin = np.argmin(labels_dists, 0)[0]
dists_min = np.min(labels_dists, 0)[0]
closest_label = labels[dists_argmin].name
print('Parsing {} ({})'.format(dipole_name, closest_label))
for line in lines:
if len(line) == 0:
continue
elif len(line) != 2:
print('{}: Problem parsing "{}"'.format(lables_times_fname, line))
continue
label_name, label_time = line
label_pos = labels_dict.get(label_name, None)
if label_pos is not None:
dist_from_dipole = np.linalg.norm(dipole_pos - label_pos)
dists.append(dist_from_dipole)
else:
dist_from_dipole = -1
dists.append(np.nan)
output.append('{}: {} ({:.4f})'.format(label_name, label_time, dist_from_dipole))
for ind, dist in enumerate(dists):
if dist < dist_threshold:
output[ind] = '{} ***'.format(output[ind])
title = '{}: {} {:.4f} dist from outer skin: {:.4f} '.format(
dipole_name, closest_label, dists_min, dists_from_outer_skin)
utils.save_arr_to_file(output, output_fname, title)
def create_coloring(x, subject, atlas, conditions, colors_map='YlOrRd', exclude=['unknown', 'corpuscallosum'],
colors_min_val=None, colors_max_val=None):
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas, exclude=tuple(exclude), sorted_according_to_annot_file=True,
only_names=True)
for cond_id, cond_name in enumerate(conditions):
values = x[:, cond_id]
if colors_min_val is None:
colors_min_val = np.min(x)
if colors_max_val is None:
colors_max_val = np.max(x)
colors = utils.arr_to_colors(values, colors_min_val, colors_max_val, colors_map=colors_map)
coloring_fname = op.join(MMVT_DIR, subject, 'coloring', 'labels_{}_coloring.csv'.format(cond_name))
write_coloring_file(coloring_fname, labels, colors)
values_diff = np.squeeze(np.diff(x))
abs_max = max(map(abs, [np.max(values_diff), np.min(values_diff)]))
colors = utils.mat_to_colors(values_diff, -abs_max, abs_max, 'RdBu', flip_cm=True)
coloring_fname = op.join(MMVT_DIR, subject, 'coloring', 'labels_{}_{}_diff_coloring.csv'.format(*conditions))
write_coloring_file(coloring_fname, labels, colors)
def create_coloring(x, subject, atlas, conditions, colors_map='YlOrRd', exclude=['unknown', 'corpuscallosum'],
colors_min_val=None, colors_max_val=None):
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas, exclude=exclude, sorted_according_to_annot_file=True,
only_names=True)
for cond_id, cond_name in enumerate(conditions):
values = x[:, cond_id]
if colors_min_val is None:
colors_min_val = np.min(x)
if colors_max_val is None:
colors_max_val = np.max(x)
colors = utils.arr_to_colors(values, colors_min_val, colors_max_val, colors_map=colors_map)
coloring_fname = op.join(MMVT_DIR, subject, 'coloring', 'labels_{}_coloring.csv'.format(cond_name))
write_coloring_file(coloring_fname, labels, colors)
values_diff = np.squeeze(np.diff(x))
abs_max = max(map(abs, [np.max(values_diff), np.min(values_diff)]))
colors = utils.mat_to_colors(values_diff, -abs_max, abs_max, 'RdBu', flip_cm=True)
coloring_fname = op.join(MMVT_DIR, subject, 'coloring', 'labels_{}_{}_diff_coloring.csv'.format(*conditions))
write_coloring_file(coloring_fname, labels, colors)
def lables_stat(subject, atlas, excluded=('corpuscallosum', 'unknown')):
all_labels = lu.read_labels(subject, SUBJECTS_DIR, atlas)
labels, _ = lu.remove_exclude_labels(all_labels, excludes=excluded)
print('Remove {} labels'.format(len(all_labels) - len(labels)))
vertices_num = [len(l.vertices) for l in labels]
print('vertivces num: {}-{}'.format(np.min(vertices_num),
np.max(vertices_num)))
labels_area = []
for l in tqdm(labels):
vertices, faces = get_vertices_faces(l.vertices, subject, l.hemi)
labels_area.append(tu.triangle_area(vertices, faces))
labels_area = np.array(labels_area)
print('areas: min {}, max {}, mean {}, std {}'.format(
np.min(labels_area), np.max(labels_area), np.mean(labels_area),
np.std(labels_area)))
fol = utils.make_dir(op.join(SUBJECTS_DIR, subject, 'label', atlas))
output_fname = op.join(fol, 'labels_stat.npz')
np.savez(output_fname, labels_area=labels_area, vertices_num=vertices_num)
def calc_labels_center_of_mass(subject, atlas, read_from_annotation=True, surf_name='pial', labels_fol='', labels=None):
import csv
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas)
if len(labels) > 0:
if np.all(labels[0].pos == 0):
verts = {}
for hemi in utils.HEMIS:
verts[hemi], _ = utils.read_pial_npz(subject, MMVT_DIR, hemi)
for label in labels:
label.pos = verts[label.hemi][label.vertices]
center_of_mass = lu.calc_center_of_mass(labels)
with open(op.join(SUBJECTS_DIR, subject, 'label', '{}_center_of_mass.csv'.format(atlas)), 'w') as csvfile:
writer = csv.writer(csvfile, delimiter=',')
for label in labels:
writer.writerow([label.name, *center_of_mass[label.name]])
com_fname = op.join(SUBJECTS_DIR, subject, 'label', '{}_center_of_mass.pkl'.format(atlas))
blend_fname = op.join(MMVT_DIR, subject, '{}_center_of_mass.pkl'.format(atlas))
utils.save(center_of_mass, com_fname)
shutil.copyfile(com_fname, blend_fname)
return len(labels) > 0 and op.isfile(com_fname) and op.isfile(blend_fname)
def save_hemis_curv(subject, atlas):
out_curv_file = op.join(MMVT_DIR, subject, 'surf', '{hemi}.curv.npy')
# out_border_file = op.join(MMVT_DIR, subject, 'surf', '{hemi}.curv.borders.npy')
# if utils.both_hemi_files_exist(out_file):
# return True
for hemi in utils.HEMIS:
# Load in curvature values from the ?h.curv file.
if not op.isfile(out_curv_file.format(hemi=hemi)):
curv_path = op.join(SUBJECTS_DIR, subject, 'surf', '{}.curv'.format(hemi))
curv = nib.freesurfer.read_morph_data(curv_path)
bin_curv = np.array(curv > 0, np.int)
np.save(out_curv_file.format(hemi=hemi), bin_curv)
else:
bin_curv = np.load(out_curv_file.format(hemi=hemi))
labels_fol = op.join(MMVT_DIR, subject, 'surf', '{}_{}_curves'.format(atlas, hemi))
utils.make_dir(labels_fol)
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas, hemi=hemi)
for label in labels:
labels_curv = bin_curv[label.vertices]
np.save(op.join(labels_fol, '{}_curv.npy'.format(label.name)), labels_curv)
return utils.both_hemi_files_exist(out_curv_file) # and utils.both_hemi_files_exist(out_border_file)
def save_hemis_curv(subject, atlas):
out_curv_file = op.join(MMVT_DIR, subject, 'surf', '{hemi}.curv.npy')
# out_border_file = op.join(MMVT_DIR, subject, 'surf', '{hemi}.curv.borders.npy')
# if utils.both_hemi_files_exist(out_file):
# return True
for hemi in utils.HEMIS:
# Load in curvature values from the ?h.curv file.
if not op.isfile(out_curv_file.format(hemi=hemi)):
curv_path = op.join(SUBJECTS_DIR, subject, 'surf', '{}.curv'.format(hemi))
curv = nib.freesurfer.read_morph_data(curv_path)
bin_curv = np.array(curv > 0, np.int)
np.save(out_curv_file.format(hemi=hemi), bin_curv)
else:
bin_curv = np.load(out_curv_file.format(hemi=hemi))
labels_fol = op.join(MMVT_DIR, subject, 'surf', '{}_{}_curves'.format(atlas, hemi))
utils.make_dir(labels_fol)
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas, hemi=hemi)
for label in labels:
labels_curv = bin_curv[label.vertices]
np.save(op.join(labels_fol, '{}_curv.npy'.format(label.name)), labels_curv)
return utils.both_hemi_files_exist(out_curv_file) # and utils.both_hemi_files_exist(out_border_file)
def save_rois_connectivity(subject, args):
# atlas, mat_fname, mat_field, conditions, stat=STAT_DIFF, windows=0,
# labels_exclude=['unknown', 'corpuscallosum'], threshold=0, threshold_percentile=0,
# color_map='jet', norm_by_percentile=True, norm_percs=(1, 99), symetric_colors=True):
# args.atlas, args.mat_fname, args.mat_field, args.conditions, args.stat,
# args.windows, args.labels_exclude, args.threshold, args.threshold_percentile,
# args.color_map, args.norm_by_percentile, args.norm_percs)
d = dict()
data = sio.loadmat(args.mat_fname)[args.mat_field]
d['labels'] = lu.read_labels(
subject, SUBJECTS_DIR, args.atlas, exclude=args.labels_exclude,sorted_according_to_annot_file=True)
d['locations'] = lu.calc_center_of_mass(d['labels'], ret_mat=True) * 1000
d['hemis'] = ['rh' if l.hemi == 'rh' else 'lh' for l in d['labels']]
d['labels'] = [l.name for l in d['labels']]
(d['con_colors'], d['con_indices'], d['con_names'], d['con_values'], d['con_types'],
d['data_max'], d['data_min']) = calc_connections_colors(data, d['labels'], d['hemis'], args)
# args.stat, args.conditions, args.windows, args.threshold,
# args.threshold_percentile, args.color_map, args.norm_by_percentile, args.norm_percs, args.symetric_colors)
d['conditions'] = args.conditions
np.savez(op.join(MMVT_DIR, subject, 'rois_con'), **d)
def calc_cortical_histograms(subject,
scan_rescan,
atlas,
low_threshold=40,
high_threshold=100,
overwrite=False,
do_plot=True,
n_jobs=4):
if not lu.check_labels(subject, atlas, SUBJECTS_DIR, MMVT_DIR):
return False
output_fol = utils.make_dir(
op.join(MMVT_DIR, subject, 'ASL', scan_rescan,
'labels_hists_{}'.format(atlas)))
output_fname = op.join(MMVT_DIR, subject, 'ASL', scan_rescan,
'labels_hists_{}.pkl'.format(atlas))
if overwrite:
utils.delete_folder_files(output_fol)
print('Saving figures into {}'.format(output_fol))
labels_data = {}
for hemi in utils.HEMIS:
npy_data_fname = op.join(
MMVT_DIR, subject, 'fmri',
'fmri_CBF_{}_{}.npy'.format(scan_rescan, hemi))
if not op.isfile(npy_data_fname):
print('Cannot find hemi data file! ({})'.format(npy_data_fname))
return False
surf_fname = op.join(SUBJECTS_DIR, subject, 'surf',
'{}.pial'.format(hemi))
if not op.isfile(surf_fname):
print('Cannot find surface file! ({})'.format(surf_fname))
return False
hemi_vals = np.load(npy_data_fname)
labels = lu.read_labels(subject,
SUBJECTS_DIR,
atlas,
hemi=hemi,
n_jobs=n_jobs)
labels_vertives_num = max([max(l.vertices) for l in labels])
hemi_data_vertices_num = len(hemi_vals) - 1
if labels_vertives_num != hemi_data_vertices_num:
print(
'Wrong number of vertices or labels! labels_vertives_num ({}) != len({})'
.format(labels_vertives_num, len(hemi_vals)))
return False
for label in tqdm(labels):
fig_fname = op.join(output_fol, '{}.jpg'.format(label.name))
if op.isfile(fig_fname) and not overwrite:
continue
labels_data[label.name] = label_data = hemi_vals[label.vertices]
outliers = np.where(label_data < low_threshold)[0]
if len(outliers) > 0:
print('{} has {}/{} values < {}'.format(
label.name, len(outliers), len(label_data), low_threshold))
outliers = np.where(label_data > high_threshold)[0]
if len(outliers) > 0:
print('{} has {}/{} values > {}'.format(
label.name, len(outliers), len(label_data),
high_threshold))
label_data[label_data < low_threshold] = low_threshold
label_data[label_data > high_threshold] = high_threshold
if do_plot:
plt.hist(label_data, bins=40)
plt.savefig(fig_fname)
plt.close()
utils.save(labels_data, output_fname)
def post_meg_preproc(args):
inv_method, em, atlas = 'dSPM', 'mean_flip', 'darpa_atlas'
bands = dict(theta=[4, 8],
alpha=[8, 15],
beta=[15, 30],
gamma=[30, 55],
high_gamma=[65, 200])
norm_times = (500, 2500)
do_plot = False
subjects = args.subject
res_fol = utils.make_dir(
op.join(utils.get_parent_fol(MMVT_DIR), 'msit-ecr'))
subjects_with_results = {}
labels = lu.read_labels(subjects[0], SUBJECTS_DIR, atlas)
labels_names = [l.name for l in labels]
labels_num = len(labels_names)
epochs_max_num = 50
template_brain = 'colin27'
now = time.time()
bands_power_mmvt_all = []
for subject_ind, subject in enumerate(subjects):
utils.time_to_go(now, subject_ind, len(subjects), runs_num_to_print=1)
subjects_with_results[subject] = {}
input_fol = utils.make_dir(
op.join(MEG_DIR, subject, 'labels_induced_power'))
plots_fol = utils.make_dir(op.join(input_fol, 'plots'))
args.subject = subject
bands_power_mmvt = {'rh': {}, 'lh': {}}
for task_ind, task in enumerate(args.tasks):
task = task.lower()
input_fnames = glob.glob(
op.join(
input_fol, '{}_*_{}_{}_induced_power.npz'.format(
task, inv_method, em)))
if len(input_fnames) < 1: # labels_num:
print('No enough files for {} {}!'.format(subject, task))
subjects_with_results[subject][task] = False
continue
# input_dname = ecr_caudalanteriorcingulate-lh_dSPM_mean_flip_induced_power
# if not do_plot:
# continue
bands_power = np.empty((len(bands), labels_num, epochs_max_num))
for input_fname in input_fnames:
d = utils.Bag(np.load(input_fname)) # label_name, atlas, data
# label_power = np.empty((len(bands), epochs_num, T)) (5, 50, 3501)
label_power, label_name = d.data, d.label_name
# for band_ind in range(len(bands)):
# label_power[band_ind] /= label_power[band_ind][:, norm_times[0]:norm_times[1]].mean()
label_ind = labels_names.index(label_name)
hemi = labels[label_ind].hemi
for band_ind, band in enumerate(bands.keys()):
label_power_norm = label_power[
band_ind][:, norm_times[0]:norm_times[1]].mean(
axis=1)[:epochs_max_num]
if len(label_power_norm) != epochs_max_num:
print('{} does have {} epochs!'.format(
input_fname, len(label_power_norm)))
break
bands_power[band_ind, label_ind] = label_power_norm
if band not in bands_power_mmvt[hemi]:
bands_power_mmvt[hemi][band] = np.empty(
(len(labels_names), label_power[band_ind].shape[1],
1, len(args.tasks)))
bands_power_mmvt[hemi][band][
label_ind, :, 0,
task_ind] = label_power[band_ind].mean(axis=0)
fig_fname = op.join(plots_fol,
'power_{}_{}.jpg'.format(label_name, task))
if do_plot: # not op.isfile(fig_fname) and
times = np.arange(
0,
label_power.shape[2]) if 'times' not in d else d.times
plot_label_power(label_power, times, label_name, bands,
task, fig_fname)
for band_ind, band in enumerate(bands.keys()):
power_fname = op.join(
res_fol, subject, '{}_labels_{}_{}_{}_power.npz'.format(
task.lower(), inv_method, em, band))
np.savez(power_fname,
data=np.array(bands_power[band_ind]),
names=labels_names)
subjects_with_results[subject][task] = True
if all(subjects_with_results[subject].values()):
bands_power_mmvt_all.append(bands_power_mmvt)
else:
print('{} does not have both tasks data!'.format(subject))
labels_data_template = op.join(MMVT_DIR, template_brain, 'meg',
'labels_data_power_{}_{}_{}_{}_{}.npz'
) # task, atlas, extract_method, hemi
for hemi in utils.HEMIS:
for band_ind, band in enumerate(bands.keys()):
power = np.array([x[hemi][band]
for x in bands_power_mmvt_all]).mean(axis=0)
labels_output_fname = meg.get_labels_data_fname(
labels_data_template, inv_method, band, atlas, em, hemi)
utils.make_dir(utils.get_parent_fol(labels_output_fname))
np.savez(labels_output_fname,
data=power,
names=labels_names,
conditions=args.tasks)
have_all = len([
subject for subject, results in subjects_with_results.items()
if all(results.values())
])
print('{}/{} with all files'.format(have_all, len(subjects)))
print(subjects_with_results)
def parcelate(subject,
atlas,
hemi,
surface_type,
vertices_labels_ids_lookup=None,
overwrite_vertices_labels_lookup=False):
output_fol = op.join(MMVT_DIR, subject, 'labels',
'{}.{}.{}'.format(atlas, surface_type, hemi))
utils.make_dir(output_fol)
vtx, fac = utils.read_ply_file(
op.join(MMVT_DIR, subject, 'surf',
'{}.{}.ply'.format(hemi, surface_type)))
if vertices_labels_ids_lookup is None or overwrite_vertices_labels_lookup:
vertices_labels_ids_lookup = lu.create_vertices_labels_lookup(
subject, atlas, True, overwrite_vertices_labels_lookup)[hemi]
labels = lu.read_labels(subject, SUBJECTS_DIR, atlas, hemi=hemi)
if 'unknown-{}'.format(hemi) not in [l.name for l in labels]:
labels.append(lu.Label([], name='unknown-{}'.format(hemi), hemi=hemi))
nV = vtx.shape[0]
nF = fac.shape[0]
nL = len(labels)
# print('The number of unique labels is {}'.format(nL))
vtxL = [[] for _ in range(nL)]
facL = [[] for _ in range(nL)]
now = time.time()
for f in range(nF):
utils.time_to_go(now, f, nF, runs_num_to_print=50000)
# Current face & labels
Cfac = fac[f]
Cidx = [vertices_labels_ids_lookup[vert_ind] for vert_ind in Cfac]
# Depending on how many vertices of the current face
# are in different labels, behave differently
# nuCidx = len(np.unique(Cidx))
# if nuCidx == 1: # If all vertices share same label
# same_label = utils.all_items_equall(Cidx)
# if same_label:
if Cidx[0] == Cidx[1] == Cidx[2]:
# Add the current face to the list of faces of the
# respective label, and don't create new faces
facL[Cidx[0]] += [Cfac.tolist()]
else: # If 2 or 3 vertices are in different labels
# Create 3 new vertices at the midpoints of the 3 edges
vtxCfac = vtx[Cfac]
vtxnew = (vtxCfac + vtxCfac[[1, 2, 0]]) / 2
vtx = np.concatenate((vtx, vtxnew))
# Define 4 new faces, with care preserve normals (all CCW)
facnew = [[Cfac[0], nV, nV + 2], [nV, Cfac[1], nV + 1],
[nV + 2, nV + 1, Cfac[2]], [nV, nV + 1, nV + 2]]
# Update nV for the next loop
nV = vtx.shape[0]
# Add the new faces to their respective labels
facL[Cidx[0]] += [facnew[0]]
facL[Cidx[1]] += [facnew[1]]
facL[Cidx[2]] += [facnew[2]]
freq_Cidx = mode(Cidx)
facL[freq_Cidx] += [facnew[3]] # central face
# Having defined new faces and assigned all faces to labels, now
# select the vertices and redefine faces to use the new vertex indices
# Also, create the file for the indices
# fidx = fopen(sprintf('%s.index.csv', srfprefix), 'w');
# params = []
# for lab in range(nL):
# facL_lab = facL[lab]
# facL_lab_flat = utils.list_flatten(facL_lab)
# vidx = list(set(facL_lab_flat))
# vtxL_lab = vtx[vidx]
# params.append((facL_lab, vtxL_lab, vidx, nV, labels[lab].name, hemi, output_fol))
# utils.run_parallel(writing_ply_files_parallel, params, njobs=n_jobs)
#
ret = True
for lab in range(nL):
ret = ret and writing_ply_files(subject, surface_type, lab, facL[lab],
vtx, vtxL, labels, hemi, output_fol)
return ret
def merge_meg_connectivity(args):
inv_method, em = 'dSPM', 'mean_flip'
con_method, con_mode = 'pli2_unbiased', 'multitaper'
bands = dict(theta=[4, 8],
alpha=[8, 15],
beta=[15, 30],
gamma=[30, 55],
high_gamma=[65, 200])
threshold_perc = 90
template_con = utils.make_dir(
op.join(MMVT_DIR, args.template_brain, 'connectivity'))
output_fname = op.join(
template_con, 'rest_{}_{}_{}.npz'.format(em, con_method, con_mode))
static_output_fname = op.join(
template_con,
'meg_rest_{}_{}_{}_{}_mean.npz'.format(em, con_method, con_mode,
'{band}'))
if op.isfile(output_fname) and not args.overwrite:
print('Averaged connectivity already exist')
return True
org_tempalte_labels = lu.read_labels(args.template_brain, SUBJECTS_DIR,
args.atlas)
tempalte_labels = [
l for l in org_tempalte_labels
if lu.get_label_hemi_invariant_name(l) not in args.labels_exclude
]
include_indices = [
ind for ind, l in enumerate(org_tempalte_labels)
if lu.get_label_hemi_invariant_name(l) not in args.labels_exclude
]
all_con = None
subjects_num = 0
good_subjects = []
for subject in args.subject:
meg_con_fname = op.join(
MMVT_DIR, subject, 'connectivity',
'rest_{}_{}_{}.npz'.format(em, con_method, con_mode))
if not op.isfile(meg_con_fname):
continue
con_dict = utils.Bag(np.load(meg_con_fname))
# print('{}: con.shape {}'.format(subject, con_dict.con.shape))
if con_dict.con.shape[0] != len(org_tempalte_labels):
print('Wrong number of cortical labels!')
continue
subject_con = con_dict.con[np.ix_(include_indices, include_indices)]
if subject_con.shape[0] != len(tempalte_labels) or subject_con.shape[
1] != len(tempalte_labels):
print('Wrong number of cortical labels!')
continue
# print(np.min(subject_con), np.max(subject_con))
if np.isnan(np.max(subject_con)):
print('nan in data!')
continue
if all_con is None:
all_con = np.zeros(subject_con.shape)
for l in range(subject_con.shape[2]):
subject_con[:, :, l] = sym_mat(subject_con[:, :, l])
all_con += subject_con
subjects_num += 1
good_subjects.append(subject)
all_con /= subjects_num
np.savez(output_fname,
con=all_con,
names=[l.name for l in tempalte_labels])
for band_ind, band in enumerate(bands.keys()):
threshold = np.percentile(all_con[:, :, band_ind], threshold_perc)
np.savez(static_output_fname.format(band=band),
con=all_con[:, :, band_ind],
threshold=threshold,
labels=[l.name for l in tempalte_labels])
print('Good subjects: {}'.format(good_subjects))
