Generate a left cerebellum volume source space

Generate a volume source space of the left cerebellum and plot its vertices relative to the left cortical surface source space and the FreeSurfer segmentation file.

# Author: Alan Leggitt <alan.leggitt@ucsf.edu>
#
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.

import mne
from mne import setup_source_space, setup_volume_source_space
from mne.datasets import sample

print(__doc__)

data_path = sample.data_path()
subjects_dir = data_path / "subjects"
subject = "sample"
aseg_fname = subjects_dir / "sample" / "mri" / "aseg.mgz"

Setup the source spaces

# setup a cortical surface source space and extract left hemisphere
surf = setup_source_space(subject, subjects_dir=subjects_dir, add_dist=False)
lh_surf = surf[0]

# setup a volume source space of the left cerebellum cortex
volume_label = "Left-Cerebellum-Cortex"
sphere = (0, 0, 0, 0.12)
lh_cereb = setup_volume_source_space(
    subject,
    mri=aseg_fname,
    sphere=sphere,
    volume_label=volume_label,
    subjects_dir=subjects_dir,
    sphere_units="m",
)

# Combine the source spaces
src = surf + lh_cereb

Plot the positions of each source space

fig = mne.viz.plot_alignment(
    subject=subject,
    subjects_dir=subjects_dir,
    surfaces="white",
    coord_frame="mri",
    src=src,
)
mne.viz.set_3d_view(
    fig, azimuth=180, elevation=90, distance=0.30, focalpoint=(-0.03, -0.01, 0.03)
)

You can export source positions to a NIfTI file:

>>> nii_fname = 'mne_sample_lh-cerebellum-cortex.nii'
>>> src.export_volume(nii_fname, mri_resolution=True)

And display source positions in freeview:

>>> from mne.utils import run_subprocess
>>> mri_fname = subjects_dir / "sample" / "mri" / "brain.mgz"
>>> run_subprocess(["freeview", "-v", str(mri_fname), "-v",
                    f"{aseg_fname}:colormap=lut:opacity=0.5",
                    "-v", f"{nii_fname}:colormap=jet:colorscale=0,2",
                    "--slice", "157", "75", "105"])

Estimated memory usage: 0 MB