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# -*- coding: utf-8 -*-
"""
.. _ex-cerebellum-source-space:
==============================================
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
# %%
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', mri_fname, '-v',
# '%s:colormap=lut:opacity=0.5' % aseg_fname, '-v',
# '%s:colormap=jet:colorscale=0,2' % nii_fname,
# '-slice', '157 75 105'])
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