Plot the MNE brain and helmet

This tutorial shows how to make the MNE helmet + brain image.

# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import mne

sample_path = mne.datasets.sample.data_path()
subjects_dir = sample_path / "subjects"
fname_evoked = sample_path / "MEG" / "sample" / "sample_audvis-ave.fif"
fname_inv = sample_path / "MEG" / "sample" / "sample_audvis-meg-oct-6-meg-inv.fif"
fname_trans = sample_path / "MEG" / "sample" / "sample_audvis_raw-trans.fif"
inv = mne.minimum_norm.read_inverse_operator(fname_inv)
evoked = mne.read_evokeds(
    fname_evoked,
    baseline=(None, 0),
    proj=True,
    verbose=False,
    condition="Left Auditory",
)
maps = mne.make_field_map(
    evoked,
    trans=fname_trans,
    ch_type="meg",
    subject="sample",
    subjects_dir=subjects_dir,
    upsampling=2,
)
time = 0.083
fig = mne.viz.create_3d_figure((512, 512), bgcolor="w", title="MNE helmet")
mne.viz.plot_alignment(
    evoked.info,
    subject="sample",
    subjects_dir=subjects_dir,
    fig=fig,
    trans=fname_trans,
    meg="sensors",
    eeg=False,
    surfaces="pial",
    coord_frame="mri",
)
evoked.plot_field(
    maps,
    time=time,
    fig=fig,
    time_label=None,
    vmax=5e-13,
    time_viewer=False,
)
mne.viz.set_3d_view(
    fig,
    azimuth=40,
    elevation=87,
    focalpoint=(0.0, -0.01, 0.04),
    roll=-105,
    distance=0.55,
)

Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-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.
    22494 x 22494 diagonal covariance (kind = 2) found.
    Source covariance matrix read.
    22494 x 22494 diagonal covariance (kind = 6) found.
    Orientation priors read.
    22494 x 22494 diagonal covariance (kind = 5) found.
    Depth priors read.
    Did not find the desired covariance matrix (kind = 3)
    Reading a source space...
    Computing patch statistics...
    Patch information added...
    Distance information added...
    [done]
    Reading a source space...
    Computing patch statistics...
    Patch information added...
    Distance information added...
    [done]
    2 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
Getting helmet for system 306m
Upsampling from 304 to 1216 vertices (upsampling=2)
Prepare MEG mapping...
Computing dot products for 305 coils...
Computing dot products for 1175 surface locations...
Field mapping data ready
    Preparing the mapping matrix...
    Truncating at 210/305 components to omit less than 0.0001 (9.9e-05)
Channel types:: grad: 203, mag: 102