def test_stc_to_label():
"""Test stc_to_label
"""
src = read_source_spaces(src_fname)
src_bad = read_source_spaces(src_bad_fname)
stc = read_source_estimate(stc_fname, 'sample')
os.environ['SUBJECTS_DIR'] = op.join(data_path, 'subjects')
labels1 = stc_to_label(stc, src='sample', smooth=3)
with warnings.catch_warnings(record=True) as w: # connectedness warning
warnings.simplefilter('always')
labels2 = stc_to_label(stc, src=src, smooth=3)
assert_true(len(w) == 1)
assert_true(len(labels1) == len(labels2))
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
with warnings.catch_warnings(record=True) as w: # connectedness warning
warnings.simplefilter('always')
labels_lh, labels_rh = stc_to_label(stc, src=src, smooth=3,
connected=True)
assert_true(len(w) == 1)
assert_raises(ValueError, stc_to_label, stc, 'sample', smooth=3,
connected=True)
assert_raises(RuntimeError, stc_to_label, stc, src=src_bad, connected=True)
assert_true(len(labels_lh) == 1)
assert_true(len(labels_rh) == 1)
def test_stc_to_label():
"""Test stc_to_label
"""
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
src = read_source_spaces(fwd_fname)
src_bad = read_source_spaces(src_bad_fname)
stc = read_source_estimate(stc_fname, 'sample')
os.environ['SUBJECTS_DIR'] = op.join(data_path, 'subjects')
labels1 = _stc_to_label(stc, src='sample', smooth=3)
labels2 = _stc_to_label(stc, src=src, smooth=3)
assert_equal(len(labels1), len(labels2))
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
with warnings.catch_warnings(record=True) as w: # connectedness warning
warnings.simplefilter('always')
labels_lh, labels_rh = stc_to_label(stc, src=src, smooth=True,
connected=True)
assert_true(len(w) > 0)
assert_raises(ValueError, stc_to_label, stc, 'sample', smooth=True,
connected=True)
assert_raises(RuntimeError, stc_to_label, stc, smooth=True, src=src_bad,
connected=True)
assert_equal(len(labels_lh), 1)
assert_equal(len(labels_rh), 1)
# test getting tris
tris = labels_lh[0].get_tris(src[0]['use_tris'], vertices=stc.vertices[0])
assert_raises(ValueError, spatial_tris_connectivity, tris,
remap_vertices=False)
connectivity = spatial_tris_connectivity(tris, remap_vertices=True)
assert_true(connectivity.shape[0] == len(stc.vertices[0]))
# "src" as a subject name
assert_raises(TypeError, stc_to_label, stc, src=1, smooth=False,
connected=False, subjects_dir=subjects_dir)
assert_raises(ValueError, stc_to_label, stc, src=SourceSpaces([src[0]]),
smooth=False, connected=False, subjects_dir=subjects_dir)
assert_raises(ValueError, stc_to_label, stc, src='sample', smooth=False,
connected=True, subjects_dir=subjects_dir)
assert_raises(ValueError, stc_to_label, stc, src='sample', smooth=True,
connected=False, subjects_dir=subjects_dir)
labels_lh, labels_rh = stc_to_label(stc, src='sample', smooth=False,
connected=False,
subjects_dir=subjects_dir)
assert_true(len(labels_lh) > 1)
assert_true(len(labels_rh) > 1)
# with smooth='patch'
with warnings.catch_warnings(record=True) as w: # connectedness warning
warnings.simplefilter('always')
labels_patch = stc_to_label(stc, src=src, smooth=True)
assert_equal(len(w), 1)
assert_equal(len(labels_patch), len(labels1))
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
def test_stc_to_label():
"""Test stc_to_label
"""
src = read_source_spaces(src_fname)
stc = read_source_estimate(stc_fname)
os.environ['SUBJECTS_DIR'] = op.join(data_path, 'subjects')
labels1 = stc_to_label(stc, src='sample', smooth=3)
labels2 = stc_to_label(stc, src=src, smooth=3)
assert_true(len(labels1) == len(labels2))
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
def test_stc_to_label():
"""Test stc_to_label."""
src = read_source_spaces(fwd_fname)
src_bad = read_source_spaces(src_bad_fname)
stc = read_source_estimate(stc_fname, 'sample')
os.environ['SUBJECTS_DIR'] = op.join(data_path, 'subjects')
labels1 = _stc_to_label(stc, src='sample', smooth=3)
labels2 = _stc_to_label(stc, src=src, smooth=3)
assert_equal(len(labels1), len(labels2))
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
with pytest.warns(RuntimeWarning, match='have holes'):
labels_lh, labels_rh = stc_to_label(stc, src=src, smooth=True,
connected=True)
pytest.raises(ValueError, stc_to_label, stc, 'sample', smooth=True,
connected=True)
pytest.raises(RuntimeError, stc_to_label, stc, smooth=True, src=src_bad,
connected=True)
assert_equal(len(labels_lh), 1)
assert_equal(len(labels_rh), 1)
# test getting tris
tris = labels_lh[0].get_tris(src[0]['use_tris'], vertices=stc.vertices[0])
pytest.raises(ValueError, spatial_tris_connectivity, tris,
remap_vertices=False)
connectivity = spatial_tris_connectivity(tris, remap_vertices=True)
assert (connectivity.shape[0] == len(stc.vertices[0]))
# "src" as a subject name
pytest.raises(TypeError, stc_to_label, stc, src=1, smooth=False,
connected=False, subjects_dir=subjects_dir)
pytest.raises(ValueError, stc_to_label, stc, src=SourceSpaces([src[0]]),
smooth=False, connected=False, subjects_dir=subjects_dir)
pytest.raises(ValueError, stc_to_label, stc, src='sample', smooth=False,
connected=True, subjects_dir=subjects_dir)
pytest.raises(ValueError, stc_to_label, stc, src='sample', smooth=True,
connected=False, subjects_dir=subjects_dir)
labels_lh, labels_rh = stc_to_label(stc, src='sample', smooth=False,
connected=False,
subjects_dir=subjects_dir)
assert (len(labels_lh) > 1)
assert (len(labels_rh) > 1)
# with smooth='patch'
with pytest.warns(RuntimeWarning, match='have holes'):
labels_patch = stc_to_label(stc, src=src, smooth=True)
assert len(labels_patch) == len(labels1)
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
def test_stc_to_label():
"""Test stc_to_label
"""
src = read_source_spaces(src_fname)
stc = SourceEstimate(stc_fname)
os.environ['SUBJECTS_DIR'] = op.join(data_path, 'subjects')
labels1 = stc_to_label(stc, src='sample', smooth=3)
labels2 = stc_to_label(stc, src=src, smooth=3)
assert_true(len(labels1) == len(labels2))
for l1, l2 in zip(labels1, labels2):
for key in l1.keys():
if key in ['comment', 'hemi']:
assert_true(l1[key] == l1[key])
else:
assert_array_almost_equal(l1[key], l2[key], 4)
def apply_rois(fn_stc, tmin, tmax, thr, min_subject='fsaverage'):
#fn_avg = subjects_dir+'/fsaverage/%s_ROIs/%s-lh.stc' %(method,evt_st)
stc_avg = mne.read_source_estimate(fn_stc)
stc_avg = stc_avg.crop(tmin, tmax)
src_pow = np.sum(stc_avg.data ** 2, axis=1)
stc_avg.data[src_pow < np.percentile(src_pow, thr)] = 0.
fn_src = subjects_dir+'/%s/bem/fsaverage-ico-5-src.fif' %min_subject
src_inv = mne.read_source_spaces(fn_src)
func_labels_lh, func_labels_rh = mne.stc_to_label(
stc_avg, src=src_inv, smooth=True,
subjects_dir=subjects_dir,
connected=True)
# Left hemisphere definition
i = 0
labels_path = fn_stc[:fn_stc.rfind('-')] + '/ini'
reset_directory(labels_path)
while i < len(func_labels_lh):
func_label = func_labels_lh[i]
func_label.save(labels_path + '/ROI_%d' %(i))
i = i + 1
# right hemisphere definition
j = 0
while j < len(func_labels_rh):
func_label = func_labels_rh[j]
func_label.save(labels_path + '/ROI_%d' %(j))
j = j + 1
def apply_rois(fn_stc, event, tmin=0.0, tmax=0.3, min_subject='fsaverage', thr=99):
"""
Compute regions of interest (ROI) based on events
----------
fn_stc : string
evoked and morphed STC.
event: string
event of the related STC.
tmin, tmax: float
segment for ROIs definition.
min_subject: string
the subject as the common brain space.
thr: float or int
threshold of STC used for ROI identification.
"""
fnlist = get_files_from_list(fn_stc)
# loop across all filenames
for ifn_stc in fnlist:
subjects_dir = os.environ['SUBJECTS_DIR']
# extract the subject infromation from the file name
stc_path = os.path.split(ifn_stc)[0]
#name = os.path.basename(fn_stc)
#tri = name.split('_')[1].split('-')[0]
min_path = subjects_dir + '/%s' % min_subject
fn_src = min_path + '/bem/fsaverage-ico-4-src.fif'
# Make sure the target path is exist
labels_path = stc_path + '/%s/' %event
reset_directory(labels_path)
# Read the MNI source space
src_inv = mne.read_source_spaces(fn_src)
stc = mne.read_source_estimate(ifn_stc, subject=min_subject)
bc_stc = stc.copy().crop(tmin, tmax)
src_pow = np.sum(bc_stc.data ** 2, axis=1)
bc_stc.data[src_pow < np.percentile(src_pow, thr)] = 0.
#stc_data = stc_morph.data
#import pdb
#pdb.set_trace()
#zscore stc for ROIs estimation
#d_mu = stc_data.mean(axis=1, keepdims=True)
#d_std = stc_data.std(axis=1, ddof=1, keepdims=True)
#z_data = (stc_data - d_mu)/d_std
func_labels_lh, func_labels_rh = mne.stc_to_label(
bc_stc, src=src_inv, smooth=True,
subjects_dir=subjects_dir,
connected=True)
# Left hemisphere definition
i = 0
while i < len(func_labels_lh):
func_label = func_labels_lh[i]
func_label.save(labels_path + '%s_%s' % (event, str(i)))
i = i + 1
# right hemisphere definition
j = 0
while j < len(func_labels_rh):
func_label = func_labels_rh[j]
func_label.save(labels_path + '%s_%s' % (event, str(j)))
j = j + 1
def apply_rois(fn_stc_list, event, min_subject='fsaverage', thr=0.85):
"""
Compute regions of interest (ROI) based on events
----------
fn_stc : string
evoked and morphed STC.
event: string
event of the related STC.
tmin, tmax: float
segment for ROIs definition.
min_subject: string
the subject as the common brain space.
thr: float or int
threshold of STC used for ROI identification.
"""
#from scipy.signal import detrend
#from scipy.stats.mstats import zscore
fnlist = get_files_from_list(fn_stc_list)
# loop across all filenames
for fn_stc in fnlist:
# extract the subject infromation from the file name
stc_path = os.path.split(fn_stc)[0]
min_path = subjects_dir + '/%s' % min_subject
fn_src = min_path + '/bem/fsaverage-ico-5-src.fif'
# Make sure the target path is exist
labels_path = stc_path + '/%s/ini' %event
reset_directory(labels_path)
# Read the MNI source space
stc = mne.read_source_estimate(fn_stc)
src_inv = mne.read_source_spaces(fn_src)
stc.lh_data[stc.lh_data < 0.85 * np.max(stc.lh_data)] = 0
stc.rh_data[stc.rh_data < 0.8 * np.max(stc.rh_data)] = 0
#data_lh=np.squeeze(stc.lh_data)
#index_lh = np.argwhere(data_lh)
#stc.lh_data[data_lh<np.percentile(data_lh[index_lh], thr)] = 0
#data_rh=np.squeeze(stc.rh_data)
#index_rh = np.argwhere(data_rh)
#stc.rh_data[data_rh<np.percentile(data_rh[index_rh], thr)] = 0
#non_index = np.argwhere(data)
#stc.data[data<np.percentile(data[non_index], thr)] = 0
func_labels_lh, func_labels_rh = mne.stc_to_label(
stc, src=src_inv, smooth=True,
subjects_dir=subjects_dir,
connected=True)
# Left hemisphere definition
i = 0
while i < len(func_labels_lh):
func_label = func_labels_lh[i]
func_label.save(labels_path + '/%s_%d' %(event, i))
i = i + 1
# right hemisphere definition
j = 0
while j < len(func_labels_rh):
func_label = func_labels_rh[j]
func_label.save(labels_path + '/%s_%d' %(event, j))
j = j + 1
def apply_rois(fn_stcs, event='LLst', tmin=0.0, tmax=0.6, tstep=0.05, window=0.2,
fmin=4, fmax=8, thr=99, min_subject='fsaverage'):
"""
Compute regions of interest (ROI) based on events
----------
fn_stcs : the file name of morphed stc.
evt: event related with stc
thr: the percentile of stc's strength
min_subject: the subject for the common brain space.
"""
from mne import read_source_spaces
fnlist = get_files_from_list(fn_stcs)
# loop across all filenames
for fn_stc in fnlist:
name = os.path.basename(fn_stc)
subject = name.split('_')[0]
subjects_dir = os.environ['SUBJECTS_DIR']
min_dir = subjects_dir + '/%s' %min_subject
labels_path = min_dir + '/DICS_ROIs/%s/%s/' %(subject, event)
reset_directory(labels_path)
src = min_dir + '/bem/%s-ico-4-src.fif' %min_subject
src_inv = read_source_spaces(src)
stc = mne.read_source_estimate(fn_stc, subject=min_subject)
stc = stc.crop(tmin, tmax)
src_pow = np.sum(stc.data ** 2, axis=1)
stc.data[src_pow < np.percentile(src_pow, thr)] = 0.
tbeg = tmin
while tbeg < tmax:
tend = tbeg + window
win_stc = stc.copy().crop(tbeg, tend)
stc_data = win_stc.data
src_pow = np.sum(stc_data ** 2, axis=1)
win_stc.data[src_pow < np.percentile(src_pow, thr)] = 0.
func_labels_lh, func_labels_rh = mne.stc_to_label(
win_stc, src=src_inv, smooth=True,
subjects_dir=subjects_dir,
connected=True)
# Left hemisphere definition
i = 0
while i < len(func_labels_lh):
func_label = func_labels_lh[i]
func_label.save(labels_path + '%s_%s_win%.2f_%2f' % (event, str(i), tbeg, tend))
i = i + 1
# right hemisphere definition
j = 0
while j < len(func_labels_rh):
func_label = func_labels_rh[j]
func_label.save(labels_path + '%s_%s_win%2f_%2f' % (event, str(j), tbeg, tend))
j = j + 1
tbeg = tbeg + tstep
def apply_rois(fn_stcs, evt='LLst', tmin=0.05, tmax=0.25, thr=99, min_subject='fsaverage'):
"""
Compute regions of interest (ROI) based on events
----------
fn_stcs : the file name of morphed stc.
evt: event related with stc
thr: the percentile of stc's strength
min_subject: the subject for the common brain space.
"""
from mne import read_source_spaces
fnlist = get_files_from_list(fn_stcs)
# loop across all filenames
for fn_stc in fnlist:
name = os.path.basename(fn_stc)
subject = name.split('_')[0]
subjects_dir = os.environ['SUBJECTS_DIR']
min_dir = subjects_dir + '/%s' %min_subject
labels_path = min_dir + '/DICS_ROIs/%s/%s/' %(subject, evt)
reset_directory(labels_path)
src = min_dir + '/bem/%s-ico-4-src.fif' %min_subject
src_inv = read_source_spaces(src)
stc = mne.read_source_estimate(fn_stc, subject=min_subject)
stc = stc.crop(tmin, tmax)
src_pow = np.sum(stc.data ** 2, axis=1)
stc.data[src_pow < np.percentile(src_pow, thr)] = 0.
#stc_data = stc_morph.data
#import pdb
#pdb.set_trace()
#zscore stc for ROIs estimation
#d_mu = stc_data.mean(axis=1, keepdims=True)
#d_std = stc_data.std(axis=1, ddof=1, keepdims=True)
#z_data = (stc_data - d_mu)/d_std
func_labels_lh, func_labels_rh = mne.stc_to_label(
stc, src=src_inv, smooth=True,
subjects_dir=subjects_dir,
connected=True)
# Left hemisphere definition
i = 0
while i < len(func_labels_lh):
func_label = func_labels_lh[i]
func_label.save(labels_path + '%s_%s' % (evt, str(i)))
i = i + 1
# right hemisphere definition
j = 0
while j < len(func_labels_rh):
func_label = func_labels_rh[j]
func_label.save(labels_path + '%s_%s' % (evt, str(j)))
j = j + 1
def apply_rois(fn_stc, tmin, tmax, thr, min_subject='fsaverage'):
'''
Make ROIs using the common STCs.
Parameters
----------
fn_stc: string.
The path of the common STCs
tmin, tmax: float (s).
The interest time range.
thr: float or int
The percentile of STCs strength.
min_subject: string.
The common subject.
'''
stc_avg = mne.read_source_estimate(fn_stc)
stc_avg = stc_avg.crop(tmin, tmax)
src_pow = np.sum(stc_avg.data ** 2, axis=1)
stc_avg.data[src_pow < np.percentile(src_pow, thr)] = 0.
fn_src = subjects_dir+'/%s/bem/fsaverage-ico-5-src.fif' %min_subject
src_inv = mne.read_source_spaces(fn_src)
func_labels_lh, func_labels_rh = mne.stc_to_label(
stc_avg, src=src_inv, smooth=True,
subjects_dir=subjects_dir,
connected=True)
# Left hemisphere definition
i = 0
labels_path = fn_stc[:fn_stc.rfind('-')] + '/ini'
reset_directory(labels_path)
while i < len(func_labels_lh):
func_label = func_labels_lh[i]
func_label.save(labels_path + '/ROI_%d' %(i))
i = i + 1
# right hemisphere definition
j = 0
while j < len(func_labels_rh):
func_label = func_labels_rh[j]
func_label.save(labels_path + '/ROI_%d' %(j))
j = j + 1
# Set parameters data_path = "/home/custine/MEG/data/krns_kr3/" + subj + "/" + sess + "/" subjects_dir = "/mnt/file1/binder/KRNS/anatomies/surfaces/" stc_fname = data_path + "ave_projon/stc/" + subj + "_" + sess + "_" + tag + "_All_c1M-spm-lh.stc" # stc_file = '/home/custine/MEG/data/krns_kr3/9367/s5/ave_projon/stc/stc_py/9367_s5_run1_Sentence-lh.stc' #9367_s5_Noun_People_All_c1M-spm-lh.stc' stcMAT_fname = data_path + "ave_projon/stc/" + subj + "_" + sess + "_" + tag + "_All_c1M-spm-lh_AllVertices.txt" print stc_fname stc = mne.read_source_estimate(stc_fname) print stc print "Shape of STC" print np.shape(stc.data) j_labels = mne.stc_to_label(stc, src="9367", subjects_dir="/mnt/file1/binder/KRNS/anatomies/surfaces/") print "Jane Labels" print j_labels[0] print # np.savetxt(stcMAT_fname, stc.data, delimiter = ',') vert, sampLen = np.shape(stc.data) print sampLen ################################################################################################################################ #######################################All Vertices - Computations################################################################ ################################################################################################################################ # x = sampLen ## Number of samples in the data (trials) # # new = np.empty([0, x])
mean_data = np.mean(np.asarray([s.data for s in stc]), axis=0)
stc_mean = mne.SourceEstimate(
mean_data, stc[0].vertices, tmin=stc[0].tmin, tstep=stc[0].tstep)
# use the stc_mean to generate a functional label
# region growing is halted at 60% of the peak value within the
# anatomical label / ROI specified by aparc_label_name
# calc lh label
stc_mean_label = stc_mean.in_label(label_lh)
data = np.abs(stc_mean_label.data)
stc_mean_label.data[data < 0.7 * np.max(data)] = 0.
func_labels_lh, _ = mne.stc_to_label(
stc_mean_label,
src=src,
smooth=True,
subjects_dir=subjects_dir,
connected=True)
# take first as func_labels are ordered based on maximum values in stc
func_label_lh = func_labels_lh[0]
# calc rh label
stc_mean_label = stc_mean.in_label(label_rh)
data = np.abs(stc_mean_label.data)
stc_mean_label.data[data < 0.7 * np.max(data)] = 0.
_, func_labels_rh = mne.stc_to_label(
stc_mean_label,
src=src,
smooth=True,
subjects_dir=subjects_dir,
coord0 = mne.vertex_to_mni(vertices=src[0]['vertno'], hemis=0, subject='fsaverage_mne')
coord1 = mne.vertex_to_mni(vertices=src[1]['vertno'], hemis=1, subject='fsaverage_mne')
coord = np.vstack([coord0, coord1])
# store the index of the sources within min_dist of the mask voxels
b = []
for i in range(gv.shape[0]):
dist = np.sqrt((coord[:, 0] - gv[i, 0]) ** 2 + (coord[:, 1] - gv[i, 1]) ** 2 + (coord[:, 2] - gv[i, 2]) ** 2)
if min(dist) <= min_dist:
b.append(np.argmin(dist))
# create a stc with 1s for the near sources
d = np.zeros([coord.shape[0], 1])
d[b] = 1
stc = mne.SourceEstimate(d, vertices=[src[0]['vertno'], src[1]['vertno']],
tmin=0, tstep=1, subject='fsaverage_mne')
# convert the stc to a label so we can morph it per subject later
avg_label = mne.stc_to_label(stc, src=src, smooth=True, connected=False)
if len(avg_label) > 2:
raise ValueError('Found more than one label!')
data = []
for s in subjs:
# check if it's AFNI or freesurfer label
if roi.find('label') > 0:
label_dir = '/Volumes/Shaw/MEG_structural/freesurfer/%s/labels/' % s
label = mne.read_label(label_dir + roi)
roi_pretty = roi.split('.')[0]
else:
roi_pretty = roi.split('/')[-1].split('+')[0]
# right labels are normally in the second index
if avg_label[0] is not None:
label = avg_label[0].morph(subject_to=s)
import mne
import numpy as np
from scipy import stats
pval_thresh = .05
nverts_thresh = 600
b=3
src = mne.setup_source_space(subject='fsaverage',fname=None,spacing='ico5',surface='inflated')
# X will have the pvalues in 0
X = 1-np.array(all_stats[b][1])[:,None] # p-values
X[X <= 1-pval_thresh] = 0
pval_stc = mne.SourceEstimate(X, vertices=stc.vertno, tmin=0, tstep=1,subject='fsaverage')
lh_labels, rh_labels = mne.stc_to_label(pval_stc, src=src, smooth=5, connected=True)
# was having problems ot mix p-values and correlations in stc, so let's keep them separated
X = np.empty([pval_stc.data.shape[0], 2])
X[:, 0] = all_stats[b][2][0]
X[:, 1] = all_stats[b][2][1]
corr_stc = mne.SourceEstimate(X, vertices=stc.vertno, tmin=0, tstep=1,subject='fsaverage')
my_txt = ['left','right']
for idx, labels in enumerate([lh_labels, rh_labels]):
print 'Found %d seeds in %s hemisphere'%(len(labels), my_txt[idx])
good_seeds = [label for label in labels if len(label.vertices)>nverts_thresh]
num_sources = [pval_stc.in_label(label).data.shape[0] for label in good_seeds]
print '%d of those are big enough'%(len(good_seeds))
for s in range(len(good_seeds)):
print 'Seed %d: %d sources, mean 1: %.2f, mean 2: %.2f'%(s+1, num_sources[s],
np.mean(corr_stc.in_label(good_seeds[s]).data[:,0]),
def test_stc_to_label():
"""Test stc_to_label."""
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
src = read_source_spaces(fwd_fname)
src_bad = read_source_spaces(src_bad_fname)
stc = read_source_estimate(stc_fname, 'sample')
os.environ['SUBJECTS_DIR'] = op.join(data_path, 'subjects')
labels1 = _stc_to_label(stc, src='sample', smooth=3)
labels2 = _stc_to_label(stc, src=src, smooth=3)
assert_equal(len(labels1), len(labels2))
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
with warnings.catch_warnings(record=True) as w: # connectedness warning
warnings.simplefilter('always')
labels_lh, labels_rh = stc_to_label(stc,
src=src,
smooth=True,
connected=True)
assert_true(len(w) > 0)
assert_raises(ValueError,
stc_to_label,
stc,
'sample',
smooth=True,
connected=True)
assert_raises(RuntimeError,
stc_to_label,
stc,
smooth=True,
src=src_bad,
connected=True)
assert_equal(len(labels_lh), 1)
assert_equal(len(labels_rh), 1)
# test getting tris
tris = labels_lh[0].get_tris(src[0]['use_tris'], vertices=stc.vertices[0])
assert_raises(ValueError,
spatial_tris_connectivity,
tris,
remap_vertices=False)
connectivity = spatial_tris_connectivity(tris, remap_vertices=True)
assert_true(connectivity.shape[0] == len(stc.vertices[0]))
# "src" as a subject name
assert_raises(TypeError,
stc_to_label,
stc,
src=1,
smooth=False,
connected=False,
subjects_dir=subjects_dir)
assert_raises(ValueError,
stc_to_label,
stc,
src=SourceSpaces([src[0]]),
smooth=False,
connected=False,
subjects_dir=subjects_dir)
assert_raises(ValueError,
stc_to_label,
stc,
src='sample',
smooth=False,
connected=True,
subjects_dir=subjects_dir)
assert_raises(ValueError,
stc_to_label,
stc,
src='sample',
smooth=True,
connected=False,
subjects_dir=subjects_dir)
labels_lh, labels_rh = stc_to_label(stc,
src='sample',
smooth=False,
connected=False,
subjects_dir=subjects_dir)
assert_true(len(labels_lh) > 1)
assert_true(len(labels_rh) > 1)
# with smooth='patch'
with warnings.catch_warnings(record=True) as w: # connectedness warning
warnings.simplefilter('always')
labels_patch = stc_to_label(stc, src=src, smooth=True)
assert_equal(len(w), 1)
assert_equal(len(labels_patch), len(labels1))
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
def apply_rois(fn_stc, event, tmin=0.0, tmax=0.3, tstep=0.05, window=0.2,
min_subject='fsaverage', thr=99):
"""
Compute regions of interest (ROI) based on events
----------
fn_stc : string
evoked and morphed STC.
event: string
event of the related STC.
tmin, tmax: float
segment for ROIs definition.
min_subject: string
the subject as the common brain space.
thr: float or int
threshold of STC used for ROI identification.
"""
from scipy.signal import detrend
from scipy.stats.mstats import zscore
fnlist = get_files_from_list(fn_stc)
# loop across all filenames
for ifn_stc in fnlist:
subjects_dir = os.environ['SUBJECTS_DIR']
# extract the subject infromation from the file name
stc_path = os.path.split(ifn_stc)[0]
#name = os.path.basename(fn_stc)
#tri = name.split('_')[1].split('-')[0]
min_path = subjects_dir + '/%s' % min_subject
fn_src = min_path + '/bem/fsaverage-ico-4-src.fif'
# Make sure the target path is exist
labels_path = stc_path + '/%s/' %event
reset_directory(labels_path)
# Read the MNI source space
src_inv = mne.read_source_spaces(fn_src)
stc = mne.read_source_estimate(ifn_stc, subject=min_subject)
#stc = stc.crop(tmin, tmax)
#src_pow = np.sum(stc.data ** 2, axis=1)
#stc.data[src_pow < np.percentile(src_pow, thr)] = 0.
stc = stc.crop(tmin, tmax)
cal_data = stc.data
dt_data = detrend(cal_data, axis=-1)
zc_data = zscore(dt_data, axis=-1)
src_pow = np.sum(zc_data ** 2, axis=1)
stc.data[src_pow < np.percentile(src_pow, thr)] = 0.
tbeg = tmin
count = 1
while tbeg < tmax:
tend = tbeg + window
if tend > tmax:
break
win_stc = stc.copy().crop(tbeg, tend)
stc_data = win_stc.data
src_pow = np.sum(stc_data ** 2, axis=1)
win_stc.data[src_pow < np.percentile(src_pow, thr)] = 0.
func_labels_lh, func_labels_rh = mne.stc_to_label(
win_stc, src=src_inv, smooth=True,
subjects_dir=subjects_dir,
connected=True)
# Left hemisphere definition
i = 0
while i < len(func_labels_lh):
func_label = func_labels_lh[i]
func_label.save(labels_path + '%s_%s_win%d' % (event, str(i), count))
i = i + 1
# right hemisphere definition
j = 0
while j < len(func_labels_rh):
func_label = func_labels_rh[j]
func_label.save(labels_path + '%s_%s_win%d' % (event, str(j), count))
j = j + 1
tbeg = tbeg + tstep
count = count + 1
stc_mean = stc.copy().crop(tmin, tmax).mean()
# use the stc_mean to generate a functional label
# region growing is halted at 60% of the peak value within the
# anatomical label / ROI specified by aparc_label_name
label = mne.read_labels_from_annot(subject,
parc='aparc',
subjects_dir=subjects_dir,
regexp=aparc_label_name)[0]
stc_mean_label = stc_mean.in_label(label)
data = np.abs(stc_mean_label.data)
stc_mean_label.data[data < 0.6 * np.max(data)] = 0.
func_labels, _ = mne.stc_to_label(stc_mean_label,
src=src,
smooth=True,
subjects_dir=subjects_dir,
connected=True)
# take first as func_labels are ordered based on maximum values in stc
func_label = func_labels[0]
# load the anatomical ROI for comparison
anat_label = mne.read_labels_from_annot(subject,
parc='aparc',
subjects_dir=subjects_dir,
regexp=aparc_label_name)[0]
# extract the anatomical time course for each label
stc_anat_label = stc.in_label(anat_label)
pca_anat = stc.extract_label_time_course(anat_label, src, mode='pca_flip')[0]
stc_clu.subject = "fsaverage"
with open(
"{}{}clu_{}-{}Hz_{}_{}_A".format(proc_dir, stat_dir, fr[0], fr[1],
cond_str, thresh_str), "rb") as f:
f_obs, clusters, cluster_pv, H0 = pickle.load(f)
f_thresh = np.quantile(H0, 0.95)
# stc_clu = mne.stats.summarize_clusters_stc(clu,subject="fsaverage",
# p_thresh=0.05,
# vertices=stc_clu.vertices)
meta_clusts = _find_clusters(stc_clu.data[:, 0], 1e-8, connectivity=cnx)[0]
clust_labels = []
for mc in meta_clusts:
temp_stc = stc_clu.copy()
temp_stc.data[:] = np.zeros((temp_stc.data.shape[0], 1))
temp_stc.data[mc, 0] = 1
lab = [x for x in mne.stc_to_label(temp_stc, src=fs_src) if x][0]
clust_labels.append(lab)
X = np.zeros(
(len(subjs), len(clust_labels), fr[1] - fr[0] + 1, len(conds), len(wavs)))
for sub_idx, sub in enumerate(subjs):
src = mne.read_source_spaces("{}{}_{}-src.fif".format(
proc_dir, sub, spacing))
vertnos = [s["vertno"] for s in src]
morph = mne.compute_source_morph(src,
subject_from=sub_key[sub],
subject_to="fsaverage",
spacing=int(spacing[-1]),
subjects_dir=subjects_dir,
smooth=None)
n_permutations=n_permutations,
tail=0,
stat_fun=stat_fun,
connectivity=connectivity,
n_jobs=n_jobs, seed=0)
print "Time elapsed : %s (s)" % (time() - t0)
clusters = [c.reshape(n_times, n_vertices).T for c in clusters]
#you get a cluster for every single thing that crossed the first-stage threshold
# stc_log_pv_cluster = copy.deepcopy(mean_stc1)
# stc_log_pv_cluster.data = np.zeros_like(stc_log_pv_cluster.data)
# for pv, c in zip(cluster_pv, clusters):
# stc_log_pv_cluster.data[c] = -np.log10(pv)
#
# stc_log_pv_cluster.save(prefix + 'clusters_pv_%s_%s' % (stat_name, t))
stc_cluster = copy.deepcopy(template_stc)
#you only write out a cluster to an stc file if it crosses the second-stage threshold
for k, c in enumerate(clusters):
stc_cluster.data = c
if cluster_pv[k] < 0.15: ##This is the threshold for saving an stc file with cluster
stcFileName = '/cluster/kuperberg/SemPrMM/MEG/results/source_space/cluster_stats/' + prefix + '%d-%d_cluster%d_%s_thresh_%s_pv_%.3f' % (args.t1*1000,args.t2*1000,k, stat_name, t, cluster_pv[k])
stc_cluster.save(stcFileName)
#stc_cluster.save('/cluster/kuperberg/SemPrMM/MEG/results/source_space/cluster_stats/' + prefix + '%d-%d_cluster%d_%s_thresh_%s_pv_%.3f' % (args.t1*1000,args.t2*1000,k, stat_name, t, cluster_pv[k]))
labelArray = mne.stc_to_label(stc_cluster, 'fsaverage')
label = labelArray[0]
mne.write_label(stcFileName, label)
print 'pv : %s' % np.sort(cluster_pv)[:5]
binarydata[Vmask] = 1
binarydata2 = np.concatenate((np.zeros(Vmask.shape), binarydata))
stc = np.zeros((binarydata2.shape[0], 2))
stc[:, 0] = binarydata2
SrcEst_label = mne.SourceEstimate(stc,
vertices=templateSTC.vertices,
tmin=0,
tstep=templateSTC.tstep,
subject=MRIsubject)
_, RHfunclabel = mne.stc_to_label(SrcEst_label,
src=src,
smooth=True,
connected=True,
subjects_dir=subjects_dir)
del binarydata, binarydata2, stc, SrcEst_label
# make surface plot
SrcPlot = SrcEst.plot(subject=MRIsubject,
surface='inflated',
hemi='rh',
subjects_dir=subjects_dir,
time_unit='ms',
views='ven',
initial_time=round(t),
time_label=None,
colorbar=True,
size=(600, 800),
def test_stc_to_label():
"""Test stc_to_label."""
src = read_source_spaces(fwd_fname)
src_bad = read_source_spaces(src_bad_fname)
stc = read_source_estimate(stc_fname, 'sample')
os.environ['SUBJECTS_DIR'] = op.join(data_path, 'subjects')
labels1 = _stc_to_label(stc, src='sample', smooth=3)
labels2 = _stc_to_label(stc, src=src, smooth=3)
assert_equal(len(labels1), len(labels2))
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
with pytest.warns(RuntimeWarning, match='have holes'):
labels_lh, labels_rh = stc_to_label(stc,
src=src,
smooth=True,
connected=True)
pytest.raises(ValueError,
stc_to_label,
stc,
'sample',
smooth=True,
connected=True)
pytest.raises(RuntimeError,
stc_to_label,
stc,
smooth=True,
src=src_bad,
connected=True)
assert_equal(len(labels_lh), 1)
assert_equal(len(labels_rh), 1)
# test getting tris
tris = labels_lh[0].get_tris(src[0]['use_tris'], vertices=stc.vertices[0])
pytest.raises(ValueError,
spatial_tris_adjacency,
tris,
remap_vertices=False)
adjacency = spatial_tris_adjacency(tris, remap_vertices=True)
assert (adjacency.shape[0] == len(stc.vertices[0]))
# "src" as a subject name
pytest.raises(TypeError,
stc_to_label,
stc,
src=1,
smooth=False,
connected=False,
subjects_dir=subjects_dir)
pytest.raises(ValueError,
stc_to_label,
stc,
src=SourceSpaces([src[0]]),
smooth=False,
connected=False,
subjects_dir=subjects_dir)
pytest.raises(ValueError,
stc_to_label,
stc,
src='sample',
smooth=False,
connected=True,
subjects_dir=subjects_dir)
pytest.raises(ValueError,
stc_to_label,
stc,
src='sample',
smooth=True,
connected=False,
subjects_dir=subjects_dir)
labels_lh, labels_rh = stc_to_label(stc,
src='sample',
smooth=False,
connected=False,
subjects_dir=subjects_dir)
assert (len(labels_lh) > 1)
assert (len(labels_rh) > 1)
# with smooth='patch'
with pytest.warns(RuntimeWarning, match='have holes'):
labels_patch = stc_to_label(stc, src=src, smooth=True)
assert len(labels_patch) == len(labels1)
for l1, l2 in zip(labels1, labels2):
assert_labels_equal(l1, l2, decimal=4)
for i in range(gv.shape[0]):
dist = np.sqrt((coord[:, 0] - gv[i, 0])**2 +
(coord[:, 1] - gv[i, 1])**2 +
(coord[:, 2] - gv[i, 2])**2)
if min(dist) <= min_dist:
b.append(np.argmin(dist))
# create a stc with 1s for the near sources
d = np.zeros([coord.shape[0], 1])
d[b] = 1
stc = mne.SourceEstimate(d,
vertices=[src[0]['vertno'], src[1]['vertno']],
tmin=0,
tstep=1,
subject='fsaverage_mne')
# convert the stc to a label so we can morph it per subject later
avg_label = mne.stc_to_label(stc, src=src, smooth=True, connected=False)
if len(avg_label) > 2:
raise ValueError('Found more than one label!')
data = []
for s in subjs:
# check if it's AFNI or freesurfer label
if roi.find('label') > 0:
label_dir = '/Volumes/Shaw/MEG_structural/freesurfer/%s/labels/' % s
label = mne.read_label(label_dir + roi)
roi_pretty = roi.split('.')[0]
else:
roi_pretty = roi.split('/')[-1].split('+')[0]
# right labels are normally in the second index
if avg_label[0] is not None:
label = avg_label[0].morph(subject_to=s)
stcs_slow_v1 = apply_inverse_epochs(slow_epo_isi,
inverse_operator,
lambda2,
method='sLORETA',
pick_ori="normal",
label=v1_label)
stcs_slow_mt = apply_inverse_epochs(slow_epo_isi,
inverse_operator,
lambda2,
method='sLORETA',
pick_ori="normal",
label=mt_label)
src = inverse_operator['src'] # the source space used
stc_label_v1 = mne.stc_to_label(stcs_slow_v1[0],
src=src,
subjects_dir=subjects_dir,
smooth=False)
stc_label_mt = mne.stc_to_label(stcs_slow_mt[0],
src=src,
subjects_dir=subjects_dir,
smooth=False)
vertices_v1 = range(len(stc_label_v1[0].vertices))
vertices_mt = range(len(stc_label_mt[0].vertices))
psi_slow_v1_mt_all = np.zeros([len(vertices_v1), len(vertices_mt), 1])
for vert_num_v1 in vertices_v1:
#one
stcs_slow = apply_inverse_epochs(slow_epo_isi,
#temp = temp3.in_label(TPOJ1_label_lh)
#w_vertices = np.unique(np.append(w_vertices, temp.vertices[0]))
""" V1 """
temp = temp3.in_label(V1_label_lh)
v1_vertices = temp.vertices[0]
###############################################################################
""" Just to visualize the new ROI """
mask = np.logical_and(times >= 0.08, times <= 0.12)
lh_label = temp3.in_label(V1_label_lh)
data = np.max(lh_label.data[:,mask],axis=1)
lh_label.data[data < 1.72] = 0.
temp_labels, _ = mne.stc_to_label(lh_label, src='fsaverage', smooth=False,
subjects_dir=fs_dir, connected=False)
temp = temp3.in_label(temp_labels)
v1_vertices = temp.vertices[0]
new_label = mne.Label(v1_vertices, hemi='lh')
brain3_1.add_label(new_label, borders=True, color='k')
###############################################################################
mask = np.logical_and(times >= 0.38, times <= 0.42)
lh_label = temp3.in_label(TE2p_label_lh)
data = np.mean(lh_label.data[:,mask],axis=1)
lh_label.data[data < 1.72] = 0.
temp_labels, _ = mne.stc_to_label(lh_label, src='fsaverage', smooth=False,
subjects_dir=fs_dir, connected=False)
temp = temp3.in_label(temp_labels)
ventral_vertices = temp.vertices[0]
src = mne.setup_source_space(subject='fsaverage',
fname=None,
spacing='ico5',
surface='inflated')
# X will have the pvalues in 0
X = 1 - np.array(all_stats[b][1])[:, None] # p-values
X[X <= 1 - pval_thresh] = 0
pval_stc = mne.SourceEstimate(X,
vertices=stc.vertno,
tmin=0,
tstep=1,
subject='fsaverage')
lh_labels, rh_labels = mne.stc_to_label(pval_stc,
src=src,
smooth=5,
connected=True)
# was having problems ot mix p-values and correlations in stc, so let's keep them separated
X = np.empty([pval_stc.data.shape[0], 2])
X[:, 0] = all_stats[b][2][0]
X[:, 1] = all_stats[b][2][1]
corr_stc = mne.SourceEstimate(X,
vertices=stc.vertno,
tmin=0,
tstep=1,
subject='fsaverage')
my_txt = ['left', 'right']
for idx, labels in enumerate([lh_labels, rh_labels]):
print 'Found %d seeds in %s hemisphere' % (len(labels), my_txt[idx])
good_seeds = [
stc_mean = stc.copy().crop(tmin, tmax).mean()
# use the stc_mean to generate a functional label
# region growing is halted at 60% of the peak value within the
# anatomical label / ROI specified by aparc_label_name
label = mne.read_labels_from_annot(subject, parc='aparc',
subjects_dir=subjects_dir,
regexp=aparc_label_name)[0]
stc_mean_label = stc_mean.in_label(label)
data = np.abs(stc_mean_label.data)
stc_mean_label.data[data < 0.6 * np.max(data)] = 0.
# 8.5% of original source space vertices were omitted during forward
# calculation, suppress the warning here with verbose='error'
func_labels, _ = mne.stc_to_label(stc_mean_label, src=src, smooth=True,
subjects_dir=subjects_dir, connected=True,
verbose='error')
# take first as func_labels are ordered based on maximum values in stc
func_label = func_labels[0]
# load the anatomical ROI for comparison
anat_label = mne.read_labels_from_annot(subject, parc='aparc',
subjects_dir=subjects_dir,
regexp=aparc_label_name)[0]
# extract the anatomical time course for each label
stc_anat_label = stc.in_label(anat_label)
pca_anat = stc.extract_label_time_course(anat_label, src, mode='pca_flip')[0]
stc_func_label = stc.in_label(func_label)
stcs_v1 = apply_inverse_epochs(allepochs,
inverse_operator,
lambda2,
method='sLORETA',
pick_ori="normal",
label=v1_label)
stcs_v4 = apply_inverse_epochs(allepochs,
inverse_operator,
lambda2,
method='sLORETA',
pick_ori="normal",
label=v4_label)
src = inverse_operator['src'] # the source space used
stc_label_v1 = mne.stc_to_label(stcs_v1[0],
src=src,
subjects_dir=subjects_dir,
smooth=False)
stc_label_v4 = mne.stc_to_label(stcs_v4[0],
src=src,
subjects_dir=subjects_dir,
smooth=False)
vertices_v1 = range(len(stc_label_v1[1].vertices))
vertices_v4 = range(len(stc_label_v4[1].vertices))
tcs_v1 = []
tcs_v4 = []
for vert_num_v1 in vertices_v1:
#one
stc_sub = stc.copy().mean()
data = np.zeros(stc_sub.data.shape)
data[:, 0] = stc.data[:, 0]
abs_data = abs(data)
#data[abs_data<np.percentile(abs_data, thr)] = 0
print np.argwhere(abs_data).shape[0]
#abs_data[abs_data < thr] = 0
#print 'time_duration:%.3f' %np.percentile(abs_data[np.where(abs_data)], thr)
#abs_data[abs_data < np.percentile(abs_data[np.where(abs_data)], thr)] = 0
abs_data[abs_data < np.percentile(abs_data, thr)] = 0
print np.argwhere(abs_data).shape[0]
stc_sub.data.setfield(abs_data, np.float32)
#stc.data.setfield(data, np.float32)
lh_labels, rh_labels = mne.stc_to_label(stc_sub,
src=src,
smooth=True,
subjects_dir=subjects_dir,
connected=True)
i = 0
while i < len(lh_labels):
lh_label = lh_labels[i]
print 'left hemisphere ROI_%d has %d vertices' % (
i, lh_label.vertices.shape[0])
dist = src[0]['dist']
label_dist = dist[lh_label.vertices, :][:, lh_label.vertices]
max_dist = round(label_dist.max() * 1000)
if max_dist > vert_size:
lh_label.save(labels_path + 'ini/%s,%s_%s' %
(side, conf_type, str(i)))
i = i + 1
stc = apply_inverse(evoked, inverse_operator, lambda2, method,
pick_normal=True)
# Make an STC in the time interval of interest and take the mean
stc_mean = stc.copy().crop(tmin, tmax).mean()
# use the stc_mean to generate a functional label
# region growing is halted at 60% of the peak value within the
# anatomical label / ROI specified by aparc_label_name
label = mne.labels_from_parc(subject, parc='aparc', subjects_dir=subjects_dir,
regexp=aparc_label_name)[0][0]
stc_mean_label = stc_mean.in_label(label)
data = np.abs(stc_mean_label.data)
stc_mean_label.data[data < 0.6 * np.max(data)] = 0.
func_labels, _ = mne.stc_to_label(stc_mean_label, src=src, smooth=5,
subjects_dir=subjects_dir, connected=True)
# take first as func_labels are ordered based on maximum values in stc
func_label = func_labels[0]
# load the anatomical ROI for comparison
anat_label = mne.labels_from_parc(subject, parc='aparc',
subjects_dir=subjects_dir,
regexp=aparc_label_name)[0][0]
# extract the anatomical time course for each label
stc_anat_label = stc.in_label(anat_label)
pca_anat = stc.extract_label_time_course(anat_label, src, mode='pca_flip')[0]
stc_func_label = stc.in_label(func_label)
pca_func = stc.extract_label_time_course(func_label, src, mode='pca_flip')[0]
stc = mne.read_source_estimate(fn_stc, subject=min_subject)
stc = stc.crop(tmin, tmax)
src_pow = np.sum(stc.data ** 2, axis=1)
stc.data[src_pow < np.percentile(src_pow, thr)] = 0.
tbeg = tmin
count = 1
while tbeg < tmax:
tend = tbeg + window
if tend > tmax:
break
win_stc = stc.copy().crop(tbeg, tend)
stc_data = win_stc.data
src_pow = np.sum(stc_data ** 2, axis=1)
win_stc.data[src_pow < np.percentile(src_pow, thr)] = 0.
func_labels_lh, func_labels_rh = mne.stc_to_label(
win_stc, src=src_inv, smooth=True, connected=True,
subjects_dir=subjects_dir)
# Left hemisphere definition
i = 0
while i < len(func_labels_lh):
func_label = func_labels_lh[i]
func_label.save(labels_path + '%s_%s_win%d' % (event, str(i), count))
i = i + 1
# right hemisphere definition
j = 0
while j < len(func_labels_rh):
func_label = func_labels_rh[j]
func_label.save(labels_path + '%s_%s_win%d' % (event, str(j), count))
j = j + 1
tbeg = tbeg + tstep
count = count + 1