Note

Click here to download the full example code

# Compute MNE inverse solution on evoked data in a mixed source space¶

Create a mixed source space and compute MNE inverse solution on an evoked dataset.

```
# Author: Annalisa Pascarella <a.pascarella@iac.cnr.it>
#
# License: BSD (3-clause)
import os.path as op
import matplotlib.pyplot as plt
from nilearn import plotting
import mne
from mne.minimum_norm import make_inverse_operator, apply_inverse
# Set dir
data_path = mne.datasets.sample.data_path()
subject = 'sample'
data_dir = op.join(data_path, 'MEG', subject)
subjects_dir = op.join(data_path, 'subjects')
bem_dir = op.join(subjects_dir, subject, 'bem')
# Set file names
fname_mixed_src = op.join(bem_dir, '%s-oct-6-mixed-src.fif' % subject)
fname_aseg = op.join(subjects_dir, subject, 'mri', 'aseg.mgz')
fname_model = op.join(bem_dir, '%s-5120-bem.fif' % subject)
fname_bem = op.join(bem_dir, '%s-5120-bem-sol.fif' % subject)
fname_evoked = data_dir + '/sample_audvis-ave.fif'
fname_trans = data_dir + '/sample_audvis_raw-trans.fif'
fname_fwd = data_dir + '/sample_audvis-meg-oct-6-mixed-fwd.fif'
fname_cov = data_dir + '/sample_audvis-shrunk-cov.fif'
```

Set up our source space.

```
# List substructures we are interested in. We select only the
# sub structures we want to include in the source space
labels_vol = ['Left-Amygdala',
'Left-Thalamus-Proper',
'Left-Cerebellum-Cortex',
'Brain-Stem',
'Right-Amygdala',
'Right-Thalamus-Proper',
'Right-Cerebellum-Cortex']
# Get a surface-based source space, here with few source points for speed
# in this demonstration, in general you should use oct6 spacing!
src = mne.setup_source_space(subject, spacing='oct5',
add_dist=False, subjects_dir=subjects_dir)
# Now we create a mixed src space by adding the volume regions specified in the
# list labels_vol. First, read the aseg file and the source space bounds
# using the inner skull surface (here using 10mm spacing to save time,
# we recommend something smaller like 5.0 in actual analyses):
vol_src = mne.setup_volume_source_space(
subject, mri=fname_aseg, pos=10.0, bem=fname_model,
volume_label=labels_vol, subjects_dir=subjects_dir,
add_interpolator=False, # just for speed, usually this should be True
verbose=True)
# Generate the mixed source space
src += vol_src
# Visualize the source space.
src.plot(subjects_dir=subjects_dir)
n = sum(src[i]['nuse'] for i in range(len(src)))
print('the src space contains %d spaces and %d points' % (len(src), n))
```

Out:

```
Setting up the source space with the following parameters:
SUBJECTS_DIR = /home/circleci/mne_data/MNE-sample-data/subjects
Subject = sample
Surface = white
Octahedron subdivision grade 5
>>> 1. Creating the source space...
Doing the octahedral vertex picking...
Loading /home/circleci/mne_data/MNE-sample-data/subjects/sample/surf/lh.white...
Mapping lh sample -> oct (5) ...
Triangle neighbors and vertex normals...
Loading geometry from /home/circleci/mne_data/MNE-sample-data/subjects/sample/surf/lh.sphere...
Setting up the triangulation for the decimated surface...
loaded lh.white 1026/155407 selected to source space (oct = 5)
Loading /home/circleci/mne_data/MNE-sample-data/subjects/sample/surf/rh.white...
Mapping rh sample -> oct (5) ...
Triangle neighbors and vertex normals...
Loading geometry from /home/circleci/mne_data/MNE-sample-data/subjects/sample/surf/rh.sphere...
Setting up the triangulation for the decimated surface...
loaded rh.white 1026/156866 selected to source space (oct = 5)
You are now one step closer to computing the gain matrix
BEM : /home/circleci/mne_data/MNE-sample-data/subjects/sample/bem/sample-5120-bem.fif
grid : 10.0 mm
mindist : 5.0 mm
MRI volume : /home/circleci/mne_data/MNE-sample-data/subjects/sample/mri/aseg.mgz
Loaded inner skull from /home/circleci/mne_data/MNE-sample-data/subjects/sample/bem/sample-5120-bem.fif (2562 nodes)
Surface CM = ( 0.7 -10.0 44.3) mm
Surface fits inside a sphere with radius 91.8 mm
Surface extent:
x = -66.7 ... 68.8 mm
y = -88.0 ... 79.0 mm
z = -44.5 ... 105.8 mm
Grid extent:
x = -70.0 ... 70.0 mm
y = -90.0 ... 80.0 mm
z = -50.0 ... 110.0 mm
4590 sources before omitting any.
2961 sources after omitting infeasible sources not within 0.0 - 91.8 mm.
Selecting voxels from Left-Amygdala
2 sources remaining after excluding sources too far from VOI voxels
Source spaces are in MRI coordinates.
Checking that the sources are inside the surface and at least 5.0 mm away (will take a few...)
Skipping interior check for 2 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
2 sources remaining after excluding the sources outside the surface and less than 5.0 mm inside.
Adjusting the neighborhood info.
Selecting voxels from Left-Thalamus-Proper
9 sources remaining after excluding sources too far from VOI voxels
Source spaces are in MRI coordinates.
Checking that the sources are inside the surface and at least 5.0 mm away (will take a few...)
Skipping interior check for 9 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
9 sources remaining after excluding the sources outside the surface and less than 5.0 mm inside.
Adjusting the neighborhood info.
Selecting voxels from Left-Cerebellum-Cortex
48 sources remaining after excluding sources too far from VOI voxels
Source spaces are in MRI coordinates.
Checking that the sources are inside the surface and at least 5.0 mm away (will take a few...)
Skipping interior check for 1 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 2 points using Qhull
3 source space points omitted because they are outside the inner skull surface.
12 source space points omitted because of the 5.0-mm distance limit.
33 sources remaining after excluding the sources outside the surface and less than 5.0 mm inside.
Adjusting the neighborhood info.
Selecting voxels from Brain-Stem
21 sources remaining after excluding sources too far from VOI voxels
Source spaces are in MRI coordinates.
Checking that the sources are inside the surface and at least 5.0 mm away (will take a few...)
Skipping interior check for 8 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
21 sources remaining after excluding the sources outside the surface and less than 5.0 mm inside.
Adjusting the neighborhood info.
Selecting voxels from Right-Amygdala
1 sources remaining after excluding sources too far from VOI voxels
Source spaces are in MRI coordinates.
Checking that the sources are inside the surface and at least 5.0 mm away (will take a few...)
Skipping interior check for 1 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
1 sources remaining after excluding the sources outside the surface and less than 5.0 mm inside.
Adjusting the neighborhood info.
Selecting voxels from Right-Thalamus-Proper
7 sources remaining after excluding sources too far from VOI voxels
Source spaces are in MRI coordinates.
Checking that the sources are inside the surface and at least 5.0 mm away (will take a few...)
Skipping interior check for 7 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
7 sources remaining after excluding the sources outside the surface and less than 5.0 mm inside.
Adjusting the neighborhood info.
Selecting voxels from Right-Cerebellum-Cortex
53 sources remaining after excluding sources too far from VOI voxels
Source spaces are in MRI coordinates.
Checking that the sources are inside the surface and at least 5.0 mm away (will take a few...)
Skipping interior check for 1 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 4 points using Qhull
4 source space points omitted because they are outside the inner skull surface.
5 source space points omitted because of the 5.0-mm distance limit.
44 sources remaining after excluding the sources outside the surface and less than 5.0 mm inside.
Adjusting the neighborhood info.
Reading /home/circleci/mne_data/MNE-sample-data/subjects/sample/mri/aseg.mgz...
the src space contains 9 spaces and 2169 points
```

We could write the mixed source space with:

```
>>> write_source_spaces(fname_mixed_src, src, overwrite=True)
```

We can also export source positions to nift file and visualize it again:

```
nii_fname = op.join(bem_dir, '%s-mixed-src.nii' % subject)
src.export_volume(nii_fname, mri_resolution=True)
plotting.plot_img(nii_fname, cmap='nipy_spectral')
# Compute the fwd matrix
fwd = mne.make_forward_solution(
fname_evoked, fname_trans, src, fname_bem,
mindist=5.0, # ignore sources<=5mm from innerskull
meg=True, eeg=False, n_jobs=1)
leadfield = fwd['sol']['data']
print("Leadfield size : %d sensors x %d dipoles" % leadfield.shape)
src_fwd = fwd['src']
n = sum(src_fwd[i]['nuse'] for i in range(len(src_fwd)))
print('the fwd src space contains %d spaces and %d points' % (len(src_fwd), n))
# Load data
condition = 'Left Auditory'
evoked = mne.read_evokeds(fname_evoked, condition=condition,
baseline=(None, 0))
noise_cov = mne.read_cov(fname_cov)
# Compute inverse solution and for each epoch
snr = 3.0 # use smaller SNR for raw data
inv_method = 'dSPM' # sLORETA, MNE, dSPM
parc = 'aparc' # the parcellation to use, e.g., 'aparc' 'aparc.a2009s'
lambda2 = 1.0 / snr ** 2
# Compute inverse operator
inverse_operator = make_inverse_operator(evoked.info, fwd, noise_cov,
depth=None, fixed=False)
stc = apply_inverse(evoked, inverse_operator, lambda2, inv_method,
pick_ori=None)
# Get labels for FreeSurfer 'aparc' cortical parcellation with 34 labels/hemi
labels_parc = mne.read_labels_from_annot(
subject, parc=parc, subjects_dir=subjects_dir)
```

Out:

```
Reading FreeSurfer lookup table
Source space : <SourceSpaces: [<surface (lh), n_vertices=155407, n_used=1026, coordinate_frame=MRI (surface RAS)>, <surface (rh), n_vertices=156866, n_used=1026, coordinate_frame=MRI (surface RAS)>, <volume (Left-Amygdala), n_used=2, coordinate_frame=MRI (surface RAS)>, <volume (Left-Thalamus-Proper), n_used=9, coordinate_frame=MRI (surface RAS)>, <volume (Left-Cerebellum-Cortex), n_used=33, coordinate_frame=MRI (surface RAS)>, <volume (Brain-Stem), n_used=21, coordinate_frame=MRI (surface RAS)>, <volume (Right-Amygdala), n_used=1, coordinate_frame=MRI (surface RAS)>, <volume (Right-Thalamus-Proper), n_used=7, coordinate_frame=MRI (surface RAS)>, <volume (Right-Cerebellum-Cortex), n_used=44, coordinate_frame=MRI (surface RAS)>]>
MRI -> head transform : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw-trans.fif
Measurement data : sample_audvis-ave.fif
Conductor model : /home/circleci/mne_data/MNE-sample-data/subjects/sample/bem/sample-5120-bem-sol.fif
Accurate field computations
Do computations in head coordinates
Free source orientations
Read 9 source spaces a total of 2169 active source locations
Coordinate transformation: MRI (surface RAS) -> head
0.999310 0.009985 -0.035787 -3.17 mm
0.012759 0.812405 0.582954 6.86 mm
0.034894 -0.583008 0.811716 28.88 mm
0.000000 0.000000 0.000000 1.00
Read 306 MEG channels from info
99 coil definitions read
Coordinate transformation: MEG device -> head
0.991420 -0.039936 -0.124467 -6.13 mm
0.060661 0.984012 0.167456 0.06 mm
0.115790 -0.173570 0.977991 64.74 mm
0.000000 0.000000 0.000000 1.00
MEG coil definitions created in head coordinates.
Source spaces are now in head coordinates.
Setting up the BEM model using /home/circleci/mne_data/MNE-sample-data/subjects/sample/bem/sample-5120-bem-sol.fif...
Loading surfaces...
Homogeneous model surface loaded.
Loading the solution matrix...
Loaded linear_collocation BEM solution from /home/circleci/mne_data/MNE-sample-data/subjects/sample/bem/sample-5120-bem-sol.fif
Employing the head->MRI coordinate transform with the BEM model.
BEM model sample-5120-bem-sol.fif is now set up
Source spaces are in head coordinates.
Checking that the sources are inside the surface and at least 5.0 mm away (will take a few...)
Skipping interior check for 211 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
84 source space point omitted because of the 5.0-mm distance limit.
Skipping interior check for 219 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
84 source space point omitted because of the 5.0-mm distance limit.
Skipping interior check for 2 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
Skipping interior check for 9 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
Skipping interior check for 1 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
Skipping interior check for 8 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
Skipping interior check for 1 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
Skipping interior check for 7 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
Skipping interior check for 1 sources that fit inside a sphere of radius 43.6 mm
Skipping solid angle check for 0 points using Qhull
Setting up compensation data...
No compensation set. Nothing more to do.
Composing the field computation matrix...
Computing MEG at 2001 source locations (free orientations)...
Finished.
Leadfield size : 306 sensors x 6003 dipoles
the fwd src space contains 9 spaces and 2001 points
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)
365 x 365 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 59) active
info["bads"] and noise_cov["bads"] do not match, excluding bad channels from both
Computing inverse operator with 305 channels.
305 out of 306 channels remain after picking
Selected 305 channels
Whitening the forward solution.
Created an SSP operator (subspace dimension = 3)
Computing data rank from covariance with rank=None
Using tolerance 3.5e-13 (2.2e-16 eps * 305 dim * 5.2 max singular value)
Estimated rank (mag + grad): 302
MEG: rank 302 computed from 305 data channels with 3 projectors
Setting small MEG eigenvalues to zero (without PCA)
Creating the source covariance matrix
Adjusting source covariance matrix.
Computing SVD of whitened and weighted lead field matrix.
largest singular value = 4.45582
scaling factor to adjust the trace = 5.72916e+19
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 59.0% variance
Combining the current components...
dSPM...
[done]
Reading labels from parcellation...
read 34 labels from /home/circleci/mne_data/MNE-sample-data/subjects/sample/label/lh.aparc.annot
read 34 labels from /home/circleci/mne_data/MNE-sample-data/subjects/sample/label/rh.aparc.annot
```

Average the source estimates within each label of the cortical parcellation and each sub structure contained in the src space

```
src = inverse_operator['src']
label_ts = mne.extract_label_time_course(
[stc], labels_parc, src, mode='mean', allow_empty=True)
# plot the times series of 2 labels
fig, axes = plt.subplots(1)
axes.plot(1e3 * stc.times, label_ts[0][0, :], 'k', label='bankssts-lh')
axes.plot(1e3 * stc.times, label_ts[0][71, :].T, 'r', label='Brain-stem')
axes.set(xlabel='Time (ms)', ylabel='MNE current (nAm)')
axes.legend()
mne.viz.tight_layout()
```

Out:

```
Extracting time courses for 75 labels (mode: mean)
```

**Total running time of the script:** ( 0 minutes 26.638 seconds)

**Estimated memory usage:** 1298 MB