Day 37: Aligning source spaces

In case you're wondering what I've been up to all week, I got some feedback from the mne community about how
to incorporate source spaces based on volumes of interest into the existing mne code. We decided to implement
volumes of interest using the function mne.setup_volume_source_space. If you check out my pull request, you
can see the various steps I've been through to make this possible. The biggest hurdle was incorporating an
interpolation matrix. This matrix transforms vertices based on their individual vertex numbers in 3d source
space into mri space.

I won't go into detail about the process, but I've included a plot below showing how 3 different source spaces
align in mri space. The surfaces of the left and right hemispheres are in blue and green, respectively, the
whole brain volume is in red, and a volume of interest based on the left cortical white matter is in black.

In [1]:

%matplotlib inline
%load transform_workspace.py

In [3]:

import mne
from mne.datasets import sample
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D

mne.set_log_level(False)
data_path = sample.data_path()
subject = 'sample'
subjects_dir = data_path + '/subjects'
aseg_fname = subjects_dir + '/sample/mri/aseg.mgz'

# create a whole brain volume source
vol_src = mne.setup_volume_source_space(subject, mri=aseg_fname,
                                        subjects_dir=subjects_dir)

# create left and right hemisphere cortical surface sources
srf_src = mne.setup_source_space(subject, subjects_dir=subjects_dir,
                                 overwrite=True)

# create a left hemisphere white matter source
lwm_src = mne.setup_volume_source_space(subject, mri=aseg_fname,
                                       volume_label='Left-Cerebral-White-Matter')

# get the coordinates from all sources
vol_rr = vol_src[0]['rr']
ix = vol_src[0]['inuse'].astype('bool')
lh_rr = srf_src[0]['rr']
rh_rr = srf_src[1]['rr']
lwm_rr = lwm_src[0]['rr']

# plot the source spaces in 3 dimensions
ax = plt.axes(projection='3d')
ax.plot(vol_rr[ix, 0], vol_rr[ix, 1], vol_rr[ix, 2], 'r.', alpha=0.1)
ax.plot(lh_rr[:, 0], lh_rr[:, 1], lh_rr[:, 2], 'b.', alpha=0.1)
ax.plot(rh_rr[:, 0], rh_rr[:, 1], rh_rr[:, 2], 'g.', alpha=0.1)
ix = lwm_src[0]['inuse'].astype('bool')
ax.plot(lwm_rr[ix, 0], lwm_rr[ix, 1], lwm_rr[ix, 2], 'k.', alpha=0.5)

plt.show()

The add_dist parameter to mne.setup_source_space currently defaults to False, but the default will change to True in release 0.9. Specify the parameter explicitly to avoid this warning.