Note
Go to the end to download the full example code
Plot the MNE brain and helmet#
This tutorial shows how to make the MNE helmet + brain image.
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
Prepare MEG mapping...
Computing dot products for 305 coils...
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 1.3s remaining: 0.0s
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 1.3s finished
Computing dot products for 304 surface locations...
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 1.2s remaining: 0.0s
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 1.2s finished
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
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)
time = 0.083
fig = mne.viz.create_3d_figure((256, 256))
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)
mne.viz.set_3d_view(
fig, azimuth=40, elevation=87, focalpoint=(0., -0.01, 0.04), roll=-25,
distance=0.55)
Total running time of the script: ( 0 minutes 7.486 seconds)
Estimated memory usage: 56 MB