Plotting the full vector-valued MNE solution

The source space that is used for the inverse computation defines a set of dipoles, distributed across the cortex. When visualizing a source estimate, it is sometimes useful to show the dipole directions in addition to their estimated magnitude. This can be accomplished by computing a mne.VectorSourceEstimate and plotting it with stc.plot, which uses plot_vector_source_estimates() under the hood rather than plot_source_estimates().

It can also be instructive to visualize the actual dipole/activation locations in 3D space in a glass brain, as opposed to activations imposed on an inflated surface (as typically done in mne.SourceEstimate.plot()), as it allows you to get a better sense of the underlying source geometry.

# Author: Marijn van Vliet <w.m.vanvliet@gmail.com>
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import numpy as np

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

print(__doc__)

data_path = sample.data_path()
subjects_dir = data_path / "subjects"
smoothing_steps = 7

# Read evoked data
meg_path = data_path / "MEG" / "sample"
fname_evoked = meg_path / "sample_audvis-ave.fif"
evoked = mne.read_evokeds(fname_evoked, condition=0, baseline=(None, 0))

# Read inverse solution
fname_inv = meg_path / "sample_audvis-meg-oct-6-meg-inv.fif"
inv = read_inverse_operator(fname_inv)

# Apply inverse solution, set pick_ori='vector' to obtain a
# :class:`mne.VectorSourceEstimate` object
snr = 3.0
lambda2 = 1.0 / snr**2
stc = apply_inverse(evoked, inv, lambda2, "dSPM", pick_ori="vector")

# Use peak getter to move visualization to the time point of the peak magnitude
_, peak_time = stc.magnitude().get_peak(hemi="lh")

Plot the source estimate:

brain = stc.plot(
    initial_time=peak_time,
    hemi="lh",
    subjects_dir=subjects_dir,
    smoothing_steps=smoothing_steps,
)

# You can save a brain movie with:
# brain.save_movie(time_dilation=20, tmin=0.05, tmax=0.16, framerate=10,
#                  interpolation='linear', time_viewer=True)

Plot the activation in the direction of maximal power for this data:

stc_max, directions = stc.project("pca", src=inv["src"])
# These directions must by design be close to the normals because this
# inverse was computed with loose=0.2
print(
    "Absolute cosine similarity between source normals and directions: "
    f'{np.abs(np.sum(directions * inv["source_nn"][2::3], axis=-1)).mean()}'
)
brain_max = stc_max.plot(
    initial_time=peak_time,
    hemi="lh",
    subjects_dir=subjects_dir,
    time_label="Max power",
    smoothing_steps=smoothing_steps,
)

The normal is very similar:

brain_normal = stc.project("normal", inv["src"])[0].plot(
    initial_time=peak_time,
    hemi="lh",
    subjects_dir=subjects_dir,
    time_label="Normal",
    smoothing_steps=smoothing_steps,
)

You can also do this with a fixed-orientation inverse. It looks a lot like the result above because the loose=0.2 orientation constraint keeps sources close to fixed orientation:

fname_inv_fixed = meg_path / "sample_audvis-meg-oct-6-meg-fixed-inv.fif"
inv_fixed = read_inverse_operator(fname_inv_fixed)
stc_fixed = apply_inverse(evoked, inv_fixed, lambda2, "dSPM", pick_ori="vector")
brain_fixed = stc_fixed.plot(
    initial_time=peak_time,
    hemi="lh",
    subjects_dir=subjects_dir,
    smoothing_steps=smoothing_steps,
)

Estimated memory usage: 0 MB