Compute MNE-dSPM inverse solution on evoked data in volume source space

Compute dSPM inverse solution on MNE evoked dataset in a volume source space and stores the solution in a nifti file for visualisation.

# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

from nilearn.image import index_img
from nilearn.plotting import plot_stat_map

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

print(__doc__)

data_path = sample.data_path()
meg_path = data_path / "MEG" / "sample"
fname_inv = meg_path / "sample_audvis-meg-vol-7-meg-inv.fif"
fname_evoked = meg_path / "sample_audvis-ave.fif"

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

# Load data
evoked = read_evokeds(fname_evoked, condition=0, baseline=(None, 0))
inverse_operator = read_inverse_operator(fname_inv)
src = inverse_operator["src"]

# Compute inverse solution
stc = apply_inverse(evoked, inverse_operator, lambda2, method)
stc.crop(0.0, 0.2)

# Export result as a 4D nifti object
img = stc.as_volume(src, mri_resolution=False)  # set True for full MRI resolution

# Save it as a nifti file
# nib.save(img, f"mne_{method}_inverse.nii.gz")

t1_fname = data_path / "subjects" / "sample" / "mri" / "T1.mgz"

Plot with nilearn:

plot_stat_map(
    index_img(img, 61),
    str(t1_fname),
    threshold=8.0,
    title=f"{method} (t={stc.times[61]:.1f} s.)",
)

Estimated memory usage: 0 MB