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, 'mne_%s_inverse.nii.gz' % method)

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

Reading /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-ave.fif ...
    Read a total of 4 projection items:
        PCA-v1 (1 x 102) active
        PCA-v2 (1 x 102) active
        PCA-v3 (1 x 102) active
        Average EEG reference (1 x 60) active
    Found the data of interest:
        t =    -199.80 ...     499.49 ms (Left Auditory)
        0 CTF compensation matrices available
        nave = 55 - aspect type = 100
Projections have already been applied. Setting proj attribute to True.
Applying baseline correction (mode: mean)
Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-vol-7-meg-inv.fif...
    Reading inverse operator info...
    [done]
    Reading inverse operator decomposition...
    [done]
    305 x 305 full covariance (kind = 1) found.
    Read a total of 4 projection items:
        PCA-v1 (1 x 102) active
        PCA-v2 (1 x 102) active
        PCA-v3 (1 x 102) active
        Average EEG reference (1 x 60) active
    Noise covariance matrix read.
    11271 x 11271 diagonal covariance (kind = 2) found.
    Source covariance matrix read.
    Did not find the desired covariance matrix (kind = 6)
    11271 x 11271 diagonal covariance (kind = 5) found.
    Depth priors read.
    Did not find the desired covariance matrix (kind = 3)
    Reading a source space...
    [done]
    1 source spaces read
    Read a total of 4 projection items:
        PCA-v1 (1 x 102) active
        PCA-v2 (1 x 102) active
        PCA-v3 (1 x 102) active
        Average EEG reference (1 x 60) active
    Source spaces transformed to the inverse solution coordinate frame
Preparing the inverse operator for use...
    Scaled noise and source covariance from nave = 1 to nave = 55
    Created the regularized inverter
    Created an SSP operator (subspace dimension = 3)
    Created the whitener using a noise covariance matrix with rank 302 (3 small eigenvalues omitted)
    Computing noise-normalization factors (dSPM)...
[done]
Applying inverse operator to "Left Auditory"...
    Picked 305 channels from the data
    Computing inverse...
    Eigenleads need to be weighted ...
    Computing residual...
    Explained  59.7% variance
    Combining the current components...
    dSPM...
[done]

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: 269 MB