Generate a functional label from source estimatesΒΆ

Threshold source estimates and produce a functional label. The label is typically the region of interest that contains high values. Here we compare the average time course in the anatomical label obtained by FreeSurfer segmentation and the average time course from the functional label. As expected the time course in the functional label yields higher values.

# Author: Luke Bloy <luke.bloy@gmail.com>
#         Alex Gramfort <alexandre.gramfort@telecom-paristech.fr>
# License: BSD (3-clause)

import numpy as np
import matplotlib.pyplot as plt

import mne
from mne.minimum_norm import read_inverse_operator, apply_inverse
from mne.datasets import sample

print(__doc__)

data_path = sample.data_path()
subjects_dir = data_path + '/subjects'
fname_inv = data_path + '/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif'
fname_evoked = data_path + '/MEG/sample/sample_audvis-ave.fif'
subjects_dir = data_path + '/subjects'
subject = 'sample'

snr = 3.0
lambda2 = 1.0 / snr ** 2
method = "dSPM"  # use dSPM method (could also be MNE or sLORETA)

# Compute a label/ROI based on the peak power between 80 and 120 ms.
# The label bankssts-lh is used for the comparison.
aparc_label_name = 'bankssts-lh'
tmin, tmax = 0.080, 0.120

# Load data
evoked = mne.read_evokeds(fname_evoked, condition=0, baseline=(None, 0))
inverse_operator = read_inverse_operator(fname_inv)
src = inverse_operator['src']  # get the source space

# Compute inverse solution
stc = apply_inverse(evoked, inverse_operator, lambda2, method,
                    pick_ori='normal')

# 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.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_func_label = stc.in_label(func_label)
pca_func = stc.extract_label_time_course(func_label, src, mode='pca_flip')[0]

# flip the pca so that the max power between tmin and tmax is positive
pca_anat *= np.sign(pca_anat[np.argmax(np.abs(pca_anat))])
pca_func *= np.sign(pca_func[np.argmax(np.abs(pca_anat))])

plot the time courses....

plt.figure()
plt.plot(1e3 * stc_anat_label.times, pca_anat, 'k',
         label='Anatomical %s' % aparc_label_name)
plt.plot(1e3 * stc_func_label.times, pca_func, 'b',
         label='Functional %s' % aparc_label_name)
plt.legend()
plt.show()
../../_images/sphx_glr_plot_label_from_stc_001.png

plot brain in 3D with PySurfer if available

brain = stc_mean.plot(hemi='lh', subjects_dir=subjects_dir)
brain.show_view('lateral')

# show both labels
brain.add_label(anat_label, borders=True, color='k')
brain.add_label(func_label, borders=True, color='b')
../../_images/sphx_glr_plot_label_from_stc_000.png

Script output:

Updating smoothing matrix, be patient..
Smoothing matrix creation, step 1
Smoothing matrix creation, step 2
Smoothing matrix creation, step 3
Smoothing matrix creation, step 4
Smoothing matrix creation, step 5
Smoothing matrix creation, step 6
Smoothing matrix creation, step 7
Smoothing matrix creation, step 8
Smoothing matrix creation, step 9
Smoothing matrix creation, step 10
colormap: fmin=-4.88e+00 fmid=0.00e+00 fmax=4.88e+00 transparent=0

Total running time of the script: (0 minutes 3.209 seconds)

Download Python source code: plot_label_from_stc.py