def test_sensitivity_maps():
"""Test sensitivity map computation"""
fwd = mne.read_forward_solution(fwd_fname, surf_ori=True)
proj_eog = read_proj(eog_fname)
decim = 6
for ch_type in ['eeg', 'grad', 'mag']:
w = read_source_estimate(sensmap_fname % (ch_type, 'lh')).data
stc = sensitivity_map(fwd, projs=None, ch_type=ch_type,
mode='free', exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
assert_true(stc.subject == 'sample')
# let's just make sure the others run
if ch_type == 'grad':
# fixed (2)
w = read_source_estimate(sensmap_fname % (ch_type, '2-lh')).data
stc = sensitivity_map(fwd, projs=None, mode='fixed',
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
if ch_type == 'mag':
# ratio (3)
w = read_source_estimate(sensmap_fname % (ch_type, '3-lh')).data
stc = sensitivity_map(fwd, projs=None, mode='ratio',
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
if ch_type == 'eeg':
# radiality (4), angle (5), remaining (6), and dampening (7)
modes = ['radiality', 'angle', 'remaining', 'dampening']
ends = ['4-lh', '5-lh', '6-lh', '7-lh']
for mode, end in zip(modes, ends):
w = read_source_estimate(sensmap_fname % (ch_type, end)).data
stc = sensitivity_map(fwd, projs=proj_eog, mode=mode,
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
def plot_forward(fwd, sbj_id, sbj_dir):
import mne
import matplotlib.pyplot as plt
leadfield = fwd['sol']['data']
print 'Leadfield size : %d x %d' % leadfield.shape
grad_map = mne.sensitivity_map(fwd, ch_type='grad', mode='fixed')
mag_map = mne.sensitivity_map(fwd, ch_type='mag', mode='fixed')
picks_meg = mne.pick_types(fwd['info'], meg=True, eeg=False)
fig, axes = plt.subplots(1, 1, figsize=(10, 8), sharex=True)
fig.suptitle('Lead field matrix (500 dipoles only)', fontsize=14)
im = axes.imshow(leadfield[picks_meg, :500], origin='lower', aspect='auto', cmap='RdBu_r')
axes.set_title('meg'.upper())
axes.set_xlabel('sources')
axes.set_ylabel('sensors')
plt.colorbar(im, ax=axes, cmap='RdBu_r')
plt.show()
plt.figure()
plt.hist([grad_map.data.ravel(), mag_map.data.ravel()], bins=20, label=['Gradiometers', 'Magnetometers'],
color=['c', 'b'])
plt.legend()
plt.title('Normal orientation sensitivity')
plt.xlabel('sensitivity')
plt.ylabel('count')
plt.show()
grad_map.plot(subject=sbj_id, time_label='Gradiometer sensitivity', subjects_dir=sbj_dir, clim='auto')
def test_sensitivity_maps():
"""Test sensitivity map computation"""
fwd = mne.read_forward_solution(fwd_fname, surf_ori=True)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
proj_eog = read_proj(eog_fname)
decim = 6
for ch_type in ['eeg', 'grad', 'mag']:
w = read_source_estimate(sensmap_fname % (ch_type, 'lh')).data
stc = sensitivity_map(fwd,
projs=None,
ch_type=ch_type,
mode='free',
exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
assert_true(stc.subject == 'sample')
# let's just make sure the others run
if ch_type == 'grad':
# fixed (2)
w = read_source_estimate(sensmap_fname % (ch_type, '2-lh')).data
stc = sensitivity_map(fwd,
projs=None,
mode='fixed',
ch_type=ch_type,
exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
if ch_type == 'mag':
# ratio (3)
w = read_source_estimate(sensmap_fname % (ch_type, '3-lh')).data
stc = sensitivity_map(fwd,
projs=None,
mode='ratio',
ch_type=ch_type,
exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
if ch_type == 'eeg':
# radiality (4), angle (5), remaining (6), and dampening (7)
modes = ['radiality', 'angle', 'remaining', 'dampening']
ends = ['4-lh', '5-lh', '6-lh', '7-lh']
for mode, end in zip(modes, ends):
w = read_source_estimate(sensmap_fname % (ch_type, end)).data
stc = sensitivity_map(fwd,
projs=proj_eog,
mode=mode,
ch_type=ch_type,
exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
# test corner case for EEG
stc = sensitivity_map(fwd,
projs=[make_eeg_average_ref_proj(fwd['info'])],
ch_type='eeg',
exclude='bads')
def test_sensitivity_maps():
"""Test sensitivity map computation."""
fwd = read_forward_solution(fwd_fname)
fwd = convert_forward_solution(fwd, surf_ori=True)
projs = read_proj(eog_fname)
projs.extend(read_proj(ecg_fname))
decim = 6
for ch_type in ['eeg', 'grad', 'mag']:
w = read_source_estimate(sensmap_fname % (ch_type, 'lh')).data
stc = sensitivity_map(fwd,
projs=None,
ch_type=ch_type,
mode='free',
exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
assert stc.subject == 'sample'
# let's just make sure the others run
if ch_type == 'grad':
# fixed (2)
w = read_source_estimate(sensmap_fname % (ch_type, '2-lh')).data
stc = sensitivity_map(fwd,
projs=None,
mode='fixed',
ch_type=ch_type,
exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
if ch_type == 'mag':
# ratio (3)
w = read_source_estimate(sensmap_fname % (ch_type, '3-lh')).data
stc = sensitivity_map(fwd,
projs=None,
mode='ratio',
ch_type=ch_type,
exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
if ch_type == 'eeg':
# radiality (4), angle (5), remaining (6), and dampening (7)
modes = ['radiality', 'angle', 'remaining', 'dampening']
ends = ['4-lh', '5-lh', '6-lh', '7-lh']
for mode, end in zip(modes, ends):
w = read_source_estimate(sensmap_fname % (ch_type, end)).data
stc = sensitivity_map(fwd,
projs=projs,
mode=mode,
ch_type=ch_type,
exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
# test corner case for EEG
stc = sensitivity_map(fwd,
projs=[make_eeg_average_ref_proj(fwd['info'])],
ch_type='eeg',
exclude='bads')
# test corner case for projs being passed but no valid ones (#3135)
pytest.raises(ValueError, sensitivity_map, fwd, projs=None, mode='angle')
pytest.raises(RuntimeError, sensitivity_map, fwd, projs=[], mode='angle')
# test volume source space
fname = op.join(sample_path, 'sample_audvis_trunc-meg-vol-7-fwd.fif')
fwd = read_forward_solution(fname)
sensitivity_map(fwd)
def test_sensitivity_maps():
"""Test sensitivity map computation"""
fwd = mne.read_forward_solution(fwd_fname, surf_ori=True)
projs = None
proj_eog = read_proj(eog_fname)
decim = 6
for ch_type in ['eeg', 'grad', 'mag']:
w_lh = mne.read_w(sensmap_fname % (ch_type, 'lh'))
w_rh = mne.read_w(sensmap_fname % (ch_type, 'rh'))
w = np.r_[w_lh['data'], w_rh['data']]
stc = sensitivity_map(fwd, projs=projs, ch_type=ch_type,
mode='free', exclude='bads')
assert_array_almost_equal(stc.data.ravel(), w, decim)
assert_true(stc.subject == 'sample')
# let's just make sure the others run
if ch_type == 'grad':
# fixed
w_lh = mne.read_w(sensmap_fname % (ch_type, '2-lh'))
w_rh = mne.read_w(sensmap_fname % (ch_type, '2-rh'))
w = np.r_[w_lh['data'], w_rh['data']]
stc = sensitivity_map(fwd, projs=projs, mode='fixed',
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data.ravel(), w, decim)
if ch_type == 'mag':
# ratio
w_lh = mne.read_w(sensmap_fname % (ch_type, '3-lh'))
w_rh = mne.read_w(sensmap_fname % (ch_type, '3-rh'))
w = np.r_[w_lh['data'], w_rh['data']]
stc = sensitivity_map(fwd, projs=projs, mode='ratio',
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data.ravel(), w, decim)
if ch_type == 'eeg':
# radiality (4)
w_lh = mne.read_w(sensmap_fname % (ch_type, '4-lh'))
w_rh = mne.read_w(sensmap_fname % (ch_type, '4-rh'))
w = np.r_[w_lh['data'], w_rh['data']]
stc = sensitivity_map(fwd, projs=projs, mode='radiality',
ch_type=ch_type, exclude='bads')
# angle (5)
w_lh = mne.read_w(sensmap_fname % (ch_type, '5-lh'))
w_rh = mne.read_w(sensmap_fname % (ch_type, '5-rh'))
w = np.r_[w_lh['data'], w_rh['data']]
stc = sensitivity_map(fwd, projs=proj_eog, mode='angle',
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data.ravel(), w, decim)
# remaining (6)
w_lh = mne.read_w(sensmap_fname % (ch_type, '6-lh'))
w_rh = mne.read_w(sensmap_fname % (ch_type, '6-rh'))
w = np.r_[w_lh['data'], w_rh['data']]
stc = sensitivity_map(fwd, projs=proj_eog, mode='remaining',
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data.ravel(), w, decim)
# dampening (7)
w_lh = mne.read_w(sensmap_fname % (ch_type, '7-lh'))
w_rh = mne.read_w(sensmap_fname % (ch_type, '7-rh'))
w = np.r_[w_lh['data'], w_rh['data']]
stc = sensitivity_map(fwd, projs=proj_eog, mode='dampening',
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data.ravel(), w, decim)
def run():
args = sys.argv
if len(args) <= 1:
print 'Usage: run_anatomy_tutorial.sh <sample data directory>'
return
sample_dir = args[1]
subjects_dir = join(sample_dir, 'subjects')
meg_dir = join(sample_dir, 'MEG', 'sample')
os.environ['SUBJECTS_DIR'] = subjects_dir
os.environ['MEG_DIR'] = meg_dir
subject = 'sample'
bem = join(subjects_dir, subject, 'bem', 'sample-5120-bem-sol.fif')
mri = join(subjects_dir, subject, 'mri', 'T1.mgz')
fname = join(subjects_dir, subject, 'bem', 'volume-7mm-src.fif')
src = setup_volume_source_space(subject,
fname=fname,
pos=7,
mri=mri,
bem=bem,
overwrite=True,
subjects_dir=subjects_dir)
###############################################################################
# Compute forward solution a.k.a. lead field
raw = mne.io.Raw(join(meg_dir, 'sample_audvis_raw.fif'))
fwd_fname = join(meg_dir, 'sample_audvis-meg-vol-7-fwd.fif')
trans = join(meg_dir, 'sample_audvis_raw-trans.fif')
# for MEG only
fwd = make_forward_solution(raw.info,
trans=trans,
src=src,
bem=bem,
fname=fwd_fname,
meg=True,
eeg=False,
overwrite=True)
# Make a sensitivity map
smap = mne.sensitivity_map(fwd, ch_type='grad', mode='free')
smap.save(join(meg_dir, 'sample_audvis-grad-vol-7-fwd-sensmap'), ftype='w')
###############################################################################
# Compute MNE inverse operators
#
# Note: The MEG/EEG forward solution could be used for all
#
noise_cov = mne.read_cov(join(meg_dir, 'sample_audvis-cov.fif'))
inv = make_inverse_operator(raw.info, fwd, noise_cov)
fname = join(meg_dir, 'sample_audvis-meg-vol-7-meg-inv.fif')
write_inverse_operator(fname, inv)
def plot_sensitivity_maps(sub, ch_types):
fwd = sub.load_forward()
for ch_type in ch_types:
sens_map = mne.sensitivity_map(fwd, ch_type=ch_type, mode='fixed')
brain = sens_map.plot(title=f'{ch_type}-Sensitivity for {sub.name}',
subjects_dir=sub.subjects_dir,
clim=dict(lims=[0, 50, 100]))
plot_save(sub, 'sensitivity', trial=ch_type, brain=brain)
def run():
args = sys.argv
if len(args) <= 1:
print 'Usage: run_anatomy_tutorial.sh <sample data directory>'
return
sample_dir = args[1]
subjects_dir = join(sample_dir, 'subjects')
meg_dir = join(sample_dir, 'MEG', 'sample')
os.environ['SUBJECTS_DIR'] = subjects_dir
os.environ['MEG_DIR'] = meg_dir
subject = 'sample'
bem = join(subjects_dir, subject, 'bem', 'sample-5120-bem-sol.fif')
mri = join(subjects_dir, subject, 'mri', 'T1.mgz')
fname = join(subjects_dir, subject, 'bem', 'volume-7mm-src.fif')
src = setup_volume_source_space(subject, fname=fname, pos=7, mri=mri,
bem=bem, overwrite=True,
subjects_dir=subjects_dir)
###############################################################################
# Compute forward solution a.k.a. lead field
raw = mne.io.Raw(join(meg_dir, 'sample_audvis_raw.fif'))
fwd_fname = join(meg_dir, 'sample_audvis-meg-vol-7-fwd.fif')
trans = join(meg_dir, 'sample_audvis_raw-trans.fif')
# for MEG only
fwd = make_forward_solution(raw.info, trans=trans, src=src, bem=bem,
fname=fwd_fname, meg=True, eeg=False,
overwrite=True)
# Make a sensitivity map
smap = mne.sensitivity_map(fwd, ch_type='grad', mode='free')
smap.save(join(meg_dir, 'sample_audvis-grad-vol-7-fwd-sensmap'), ftype='w')
###############################################################################
# Compute MNE inverse operators
#
# Note: The MEG/EEG forward solution could be used for all
#
noise_cov = mne.read_cov(join(meg_dir, 'sample_audvis-cov.fif'))
inv = make_inverse_operator(raw.info, fwd, noise_cov)
fname = join(meg_dir, 'sample_audvis-meg-vol-7-meg-inv.fif')
write_inverse_operator(fname, inv)
def test_sensitivity_maps():
"""Test sensitivity map computation."""
fwd = mne.read_forward_solution(fwd_fname)
fwd = mne.convert_forward_solution(fwd, surf_ori=True)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
projs = read_proj(eog_fname)
projs.extend(read_proj(ecg_fname))
decim = 6
for ch_type in ['eeg', 'grad', 'mag']:
w = read_source_estimate(sensmap_fname % (ch_type, 'lh')).data
stc = sensitivity_map(fwd, projs=None, ch_type=ch_type,
mode='free', exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
assert_true(stc.subject == 'sample')
# let's just make sure the others run
if ch_type == 'grad':
# fixed (2)
w = read_source_estimate(sensmap_fname % (ch_type, '2-lh')).data
stc = sensitivity_map(fwd, projs=None, mode='fixed',
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
if ch_type == 'mag':
# ratio (3)
w = read_source_estimate(sensmap_fname % (ch_type, '3-lh')).data
stc = sensitivity_map(fwd, projs=None, mode='ratio',
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
if ch_type == 'eeg':
# radiality (4), angle (5), remaining (6), and dampening (7)
modes = ['radiality', 'angle', 'remaining', 'dampening']
ends = ['4-lh', '5-lh', '6-lh', '7-lh']
for mode, end in zip(modes, ends):
w = read_source_estimate(sensmap_fname % (ch_type, end)).data
stc = sensitivity_map(fwd, projs=projs, mode=mode,
ch_type=ch_type, exclude='bads')
assert_array_almost_equal(stc.data, w, decim)
# test corner case for EEG
stc = sensitivity_map(fwd, projs=[make_eeg_average_ref_proj(fwd['info'])],
ch_type='eeg', exclude='bads')
# test corner case for projs being passed but no valid ones (#3135)
assert_raises(ValueError, sensitivity_map, fwd, projs=None, mode='angle')
assert_raises(RuntimeError, sensitivity_map, fwd, projs=[], mode='angle')
# test volume source space
fname = op.join(sample_path, 'sample_audvis_trunc-meg-vol-7-fwd.fif')
fwd = mne.read_forward_solution(fname)
sensitivity_map(fwd)
def plot_sensitivity_map(fwd_sol,
subject,
fname_leadfield_plot,
fname_sensitvity_plot):
"""Estimates and plots sensitivity map of forward solution."""
# estimate lead field
leadfield = fwd_sol['sol']['data']
pp = PdfPages(fname_leadfield_plot)
# plot leadfield
plt.matshow(leadfield[:, :500])
plt.xlabel('sources')
plt.ylabel('sensors')
plt.title('Lead field matrix (500 dipoles only)')
pp.savefig()
plt.close()
# estimate sensitivity map for magnetometer
mag_map = mne.sensitivity_map(fwd_sol, ch_type='mag', mode='fixed')
# plot histogram of sensitivity
plt.hist(mag_map.data.ravel(),
bins=20,
label='Magnetometers')
plt.legend()
plt.title('Normal orientation sensitivity')
pp.savefig()
plt.close()
pp.close()
subjects_dir = os.environ.get('SUBJECTS_DIR')
brain = mag_map.plot(subject=subject,
time_label='Magnetometer sensitivity',
subjects_dir=subjects_dir,
fmin=0.1,
fmid=0.5,
fmax=0.9,
smoothing_steps=7)
brain.save_montage(fname_sensitvity_plot)
brain.close()
def test_sensitivity_maps():
"""Test sensitivity map computation."""
fwd = mne.read_forward_solution(fwd_fname, surf_ori=True)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
projs = read_proj(eog_fname)
projs.extend(read_proj(ecg_fname))
decim = 6
for ch_type in ["eeg", "grad", "mag"]:
w = read_source_estimate(sensmap_fname % (ch_type, "lh")).data
stc = sensitivity_map(fwd, projs=None, ch_type=ch_type, mode="free", exclude="bads")
assert_array_almost_equal(stc.data, w, decim)
assert_true(stc.subject == "sample")
# let's just make sure the others run
if ch_type == "grad":
# fixed (2)
w = read_source_estimate(sensmap_fname % (ch_type, "2-lh")).data
stc = sensitivity_map(fwd, projs=None, mode="fixed", ch_type=ch_type, exclude="bads")
assert_array_almost_equal(stc.data, w, decim)
if ch_type == "mag":
# ratio (3)
w = read_source_estimate(sensmap_fname % (ch_type, "3-lh")).data
stc = sensitivity_map(fwd, projs=None, mode="ratio", ch_type=ch_type, exclude="bads")
assert_array_almost_equal(stc.data, w, decim)
if ch_type == "eeg":
# radiality (4), angle (5), remaining (6), and dampening (7)
modes = ["radiality", "angle", "remaining", "dampening"]
ends = ["4-lh", "5-lh", "6-lh", "7-lh"]
for mode, end in zip(modes, ends):
w = read_source_estimate(sensmap_fname % (ch_type, end)).data
stc = sensitivity_map(fwd, projs=projs, mode=mode, ch_type=ch_type, exclude="bads")
assert_array_almost_equal(stc.data, w, decim)
# test corner case for EEG
stc = sensitivity_map(fwd, projs=[make_eeg_average_ref_proj(fwd["info"])], ch_type="eeg", exclude="bads")
# test corner case for projs being passed but no valid ones (#3135)
assert_raises(ValueError, sensitivity_map, fwd, projs=None, mode="angle")
assert_raises(RuntimeError, sensitivity_map, fwd, projs=[], mode="angle")
# test volume source space
fname = op.join(sample_path, "sample_audvis_trunc-meg-vol-7-fwd.fif")
fwd = mne.read_forward_solution(fname)
sensitivity_map(fwd)
def plot_sensitivity_map(fwd_sol, subject, fname_leadfield_plot,
fname_sensitvity_plot):
"""Estimates and plots sensitivity map of forward solution."""
# estimate lead field
leadfield = fwd_sol['sol']['data']
pp = PdfPages(fname_leadfield_plot)
# plot leadfield
plt.matshow(leadfield[:, :500])
plt.xlabel('sources')
plt.ylabel('sensors')
plt.title('Lead field matrix (500 dipoles only)')
pp.savefig()
plt.close()
# estimate sensitivity map for magnetometer
mag_map = mne.sensitivity_map(fwd_sol, ch_type='mag', mode='fixed')
# plot histogram of sensitivity
plt.hist(mag_map.data.ravel(), bins=20, label='Magnetometers')
plt.legend()
plt.title('Normal orientation sensitivity')
pp.savefig()
plt.close()
pp.close()
subjects_dir = os.environ.get('SUBJECTS_DIR')
brain = mag_map.plot(subject=subject,
time_label='Magnetometer sensitivity',
subjects_dir=subjects_dir,
fmin=0.1,
fmid=0.5,
fmax=0.9,
smoothing_steps=7)
brain.save_montage(fname_sensitvity_plot)
brain.close()
raw = mne.io.read_raw_edf(raw_fname, preload=True)
# Clean channel names to be able to use a standard 1005 montage
ch_names = [c.replace('.', '') for c in raw.ch_names]
raw.rename_channels({old: new for old, new in zip(raw.ch_names, ch_names)})
# Read and set the EEG electrode locations
montage = mne.channels.read_montage('standard_1005', ch_names=raw.ch_names,
transform=True)
raw.set_montage(montage)
raw.set_eeg_reference(projection=True) # needed for inverse modeling
# Check that the locations of EEG electrodes is correct with respect to MRI
mne.viz.plot_alignment(
raw.info, src=src, eeg=['original', 'projected'], trans=trans, dig=True)
##############################################################################
# Setup source space and compute forward
# --------------------------------------
fwd = mne.make_forward_solution(raw.info, trans=trans, src=src,
bem=bem, eeg=True, mindist=5.0, n_jobs=1)
print(fwd)
# for illustration purposes use fwd to compute the sensitivity map
eeg_map = mne.sensitivity_map(fwd, ch_type='eeg', mode='fixed')
eeg_map.plot(time_label='EEG sensitivity', subjects_dir=subjects_dir,
clim=dict(lims=[5, 50, 100]))
from mne.datasets import sample
print(__doc__)
data_path = sample.data_path()
subjects_dir = data_path + '/subjects'
fname = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif'
ecg_fname = data_path + '/MEG/sample/sample_audvis_ecg-proj.fif'
fwd = read_forward_solution(fname)
projs = read_proj(ecg_fname)
# take only one projection per channel type
projs = projs[::2]
# Compute sensitivity map
ssp_ecg_map = sensitivity_map(fwd, ch_type='grad', projs=projs, mode='angle')
###############################################################################
# Show sensitivity map
plt.hist(ssp_ecg_map.data.ravel())
plt.show()
args = dict(clim=dict(kind='value', lims=(0.2, 0.6, 1.)),
smoothing_steps=7,
hemi='rh',
subjects_dir=subjects_dir)
ssp_ecg_map.plot(subject='sample', time_label='ECG SSP sensitivity', **args)
bems = mne.make_bem_model(subject, conductivity=(0.3,),
subjects_dir=subjects_dir,
ico=None) # ico = None for morphed SP.
bem_sol = mne.make_bem_solution(bems)
bem_sol['surfs'][0]['coord_frame'] = 5
##############################################################################
# Now we can read the channels that we want to map to the cortical locations.
# Then we can compute the forward solution.
info = hcp.read_info(subject=subject, hcp_path=hcp_path, data_type='rest',
run_index=0)
picks = mne.pick_types(info, meg=True, ref_meg=False)
info = mne.pick_info(info, picks)
fwd = mne.make_forward_solution(info, trans=head_mri_t, bem=bem_sol,
src=src_subject)
mag_map = mne.sensitivity_map(
fwd, projs=None, ch_type='mag', mode='fixed', exclude=[], verbose=None)
##############################################################################
# we display sensitivity map on the original surface with little smoothing
# and admire the expected curvature-driven sensitivity pattern.
mag_map = mag_map.to_original_src(src_fsaverage, subjects_dir=subjects_dir)
mag_map.plot(subject='fsaverage', subjects_dir=subjects_dir,
clim=dict(kind='percent', lims=[0, 50, 99]),
smoothing_steps=2)
for run in runs:
fwds.append(
mne.read_forward_solution(
"{dir}nc_{sub}_{run}_{spacing}-fwd.fif".format(
dir=proc_dir, sub=v, run=run, spacing=spacing)))
avg_fwd = mne.average_forward_solutions(fwds)
del fwds
mne.write_forward_solution("{dir}nc_{sub}_{spacing}-fwd.fif".format(
dir=proc_dir, sub=v, spacing=spacing),
avg_fwd,
overwrite=True)
avg_fwd = mne.read_forward_solution(
"{dir}nc_{sub}_{spacing}-fwd.fif".format(dir=proc_dir,
sub=v,
spacing=spacing))
sen = mne.sensitivity_map(avg_fwd, ch_type="mag", mode="fixed")
m_to_fs = mne.compute_source_morph(sen,
subject_from=k,
subject_to="fsaverage",
spacing=int(spacing[-1]),
subjects_dir=subjects_dir,
smooth=None)
sen = m_to_fs.apply(sen)
sens.append(sen)
sen.save("{dir}nc_{sub}_{sp}_sens".format(dir=proc_dir, sub=v, sp=spacing))
sen = sens[0].copy()
for s in sens[1:]:
sen.data += s.data
sen.data /= len(sens)
sen.data[sen.data < thresh] = 0
def run():
args = sys.argv
if len(args) <= 1:
print 'Usage: run_meg_tutorial.sh <sample data directory>'
return
sample_dir = args[1]
subjects_dir = join(sample_dir, 'subjects')
meg_dir = join(sample_dir, 'MEG', 'sample')
os.environ['SUBJECTS_DIR'] = subjects_dir
os.environ['MEG_DIR'] = meg_dir
subject = 'sample'
src = setup_source_space(subject,
fname=True,
spacing='oct6',
n_jobs=2,
overwrite=True)
# If one wanted to use other source spaces, these types of options are
# available
src_fsaverage = setup_source_space('fsaverage',
fname=True,
spacing='ico5',
n_jobs=2,
overwrite=True,
add_dist=False)
morph_source_spaces(src_fsaverage, subject_to='sample')
setup_source_space(subject,
fname=True,
spacing='all',
overwrite=True,
n_jobs=2,
add_dist=False)
# Add distances to source space (if desired, takes a long time)
bem_dir = join(subjects_dir, join('sample', 'bem'))
os.rename(join(bem_dir, 'sample-oct-6-src.fif'),
join(bem_dir, 'sample-oct-6-orig-src.fif'))
new_src = add_source_space_distances(src, dist_limit=0.007)
new_src.save(join(bem_dir, 'sample-oct-6-src.fif'))
# Preprocessing
raw = mne.io.Raw(join(meg_dir, 'sample_audvis_raw.fif'), preload=True)
raw.info['bads'] = ['MEG 2443', 'EEG 053']
reject = dict(grad=3000e-13, mag=4000e-15, eeg=100e-6)
ecg_proj, _ = mne.preprocessing.compute_proj_ecg(raw,
l_freq=1,
h_freq=100,
ch_name='MEG 1531',
reject=reject)
eog_proj, _ = mne.preprocessing.compute_proj_eog(raw,
l_freq=1,
h_freq=35,
reject=reject,
no_proj=True)
events = mne.find_events(raw)
mne.write_events(join(meg_dir, 'sample_audvis_raw-eve.fif'), events)
event_id = [1, 2, 3, 4]
tmin, tmax = -0.2, 0.5
picks = mne.pick_types(raw.info, meg=True, eeg=True, stim=True, eog=True)
# Average with no filter
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks)
evoked = epochs.average()
evoked.save(join(meg_dir, 'sample_audvis-no-filter-ave.fif'))
raw.filter(l_freq=None, h_freq=40)
raw_resampled = raw.resample(150)
raw_resampled.save(join(meg_dir, 'sample_audvis_filt-0-40_raw.fif'),
overwrite=True)
raw.add_proj(ecg_proj)
raw.add_proj(eog_proj)
resampled_events = mne.find_events(raw_resampled)
mne.write_events(join(meg_dir, 'sample_audvis_filt-0-40_raw-eve.fif'),
resampled_events)
# Average with filter
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks)
evoked = epochs.average()
evoked.save(join(meg_dir, 'sample_audvis-ave.fif'))
# Compute the noise covariance matrix
noise_cov = mne.compute_raw_data_covariance(raw, picks=picks)
noise_cov.save(join(meg_dir, 'audvis.cov'))
# Compute the empty-room noise covariance matrix
ernoise_raw = mne.io.Raw(join(meg_dir, 'ernoise_raw.fif'), preload=True)
ernoise_raw.info['bads'] = ['MEG 2443']
ernoise_raw.filter(l_freq=None, h_freq=40)
picks = mne.pick_types(ernoise_raw.info,
meg=True,
eeg=True,
stim=True,
eog=True)
ernoise_cov = mne.compute_raw_data_covariance(ernoise_raw, picks=picks)
ernoise_cov.save(join(meg_dir, 'ernoise.cov'))
###############################################################################
# Compute forward solution a.k.a. lead field
trans = join(meg_dir, 'sample_audvis_raw-trans.fif')
bem = join(subjects_dir, 'sample', 'bem', 'sample-5120-bem-sol.fif')
# for MEG only
fname = join(meg_dir, 'sample_audvis-meg-oct-6-fwd.fif')
fwd_meg = mne.make_forward_solution(raw.info,
trans,
src,
bem,
fname=fname,
meg=True,
eeg=False,
mindist=5.0,
n_jobs=2,
overwrite=True)
# for EEG only
bem = join(subjects_dir, 'sample', 'bem',
'sample-5120-5120-5120-bem-sol.fif')
fname = join(meg_dir, 'sample_audvis-eeg-oct-6-fwd.fif')
fwd_eeg = mne.make_forward_solution(raw.info,
trans,
src,
bem,
fname=fname,
meg=False,
eeg=True,
mindist=5.0,
n_jobs=2,
overwrite=True)
# for both EEG and MEG
fname = join(meg_dir, 'sample_audvis-meg-eeg-oct-6-fwd.fif')
fwd = mne.make_forward_solution(raw.info,
trans,
src,
bem,
fname=fname,
meg=True,
eeg=True,
mindist=5.0,
n_jobs=2,
overwrite=True)
# Create various sensitivity maps
grad_map = mne.sensitivity_map(fwd, ch_type='grad', mode='free')
grad_map.save(join(meg_dir, 'sample_audvis-grad-oct-6-fwd-sensmap'),
ftype='w')
mag_map = mne.sensitivity_map(fwd, ch_type='mag', mode='free')
mag_map.save(join(meg_dir, 'sample_audvis-mag-oct-6-fwd-sensmap'),
ftype='w')
eeg_map = mne.sensitivity_map(fwd, ch_type='eeg', mode='free')
eeg_map.save(join(meg_dir, 'sample_audvis-eeg-oct-6-fwd-sensmap'),
ftype='w')
grad_map2 = mne.sensitivity_map(fwd, ch_type='grad', mode='fixed')
grad_map2.save(join(meg_dir, 'sample_audvis-grad-oct-6-fwd-sensmap-2'),
ftype='w')
mag_map2 = mne.sensitivity_map(fwd, ch_type='mag', mode='ratio')
mag_map2.save(join(meg_dir, 'sample_audvis-mag-oct-6-fwd-sensmap-3'),
ftype='w')
# Compute some with the EOG + ECG projectors
projs = ecg_proj + eog_proj + raw.info['projs']
for map_type in ['radiality', 'angle', 'remaining', 'dampening']:
eeg_map = mne.sensitivity_map(fwd,
projs=projs,
ch_type='eeg',
mode=map_type)
eeg_map.save(
join(meg_dir, 'sample_audvis-eeg-oct-6-fwd-sensmap-' + map_type))
###############################################################################
# Compute MNE inverse operators
#
# Note: The MEG/EEG forward solution could be used for all
#
inv_meg = make_inverse_operator(raw.info, fwd_meg, noise_cov, loose=0.2)
fname = join(meg_dir, 'sample_audvis-meg-oct-6-meg-inv.fif')
write_inverse_operator(fname, inv_meg)
inv_eeg = make_inverse_operator(raw.info, fwd_eeg, noise_cov, loose=0.2)
fname = join(meg_dir, 'sample_audvis-eeg-oct-6-eeg-inv.fif')
write_inverse_operator(fname, inv_eeg)
inv = make_inverse_operator(raw.info, fwd, noise_cov, loose=0.2)
fname = join(meg_dir, 'sample_audvis-meg-eeg-oct-6-meg-eeg-inv.fif')
write_inverse_operator(fname, inv)
# inverse operator with fixed orientation (for testing). Not implemented
#inv_fixed = make_inverse_operator(raw.info, fwd_meg, noise_cov,
# depth=None, fixed=True)
#fname = join(meg_dir, 'sample_audvis-meg-oct-6-meg-nodepth-fixed-inv.fif')
#write_inverse_operator(fname, inv_fixed)
# produce two with diagonal noise (for testing)
diag = noise_cov.as_diag()
inv_meg_diag = make_inverse_operator(raw.info, fwd_meg, diag, loose=0.2)
fname = join(meg_dir, 'sample_audvis-meg-oct-6-meg-diagnoise-inv.fif')
write_inverse_operator(fname, inv_meg_diag)
inv_eeg_diag = make_inverse_operator(raw.info, fwd, diag, loose=0.2)
fname = join(meg_dir,
'sample_audvis-meg-eeg-oct-6-meg-eeg-diagnoise-inv.fif')
write_inverse_operator(fname, inv_eeg_diag)
# Produce stc files
evoked.crop(0, 0.25)
stc_meg = apply_inverse(evoked, inv_meg, method='MNE')
stc_meg.save(join(meg_dir, 'sample_audvis-meg'))
stc_eeg = apply_inverse(evoked, inv_eeg, method='MNE')
stc_eeg.save(join(meg_dir, 'sample_audvis-eeg'))
stc = apply_inverse(evoked, inv, method='MNE')
stc.save(join(meg_dir, 'sample_audvis-meg-eeg'))
# let's also morph to fsaverage
stc_to = stc_meg.morph('fsaverage', grade=3, smooth=12)
stc_to.save(join(meg_dir, 'fsaverage_audvis-meg'))
stc_to = stc_eeg.morph('fsaverage', grade=3, smooth=12)
stc_to.save(join(meg_dir, 'fsaverage_audvis-eeg'))
stc_to = stc.morph('fsaverage', grade=3, smooth=12)
stc_to.save(join(meg_dir, 'fsaverage_audvis-meg-eeg'))
###############################################################################
# Do one dipole fitting
evoked = evoked.pick_types(meg=True, eeg=False)
evoked.crop(0.04, 0.095)
bem = join(subjects_dir, 'sample', 'bem', 'sample-5120-bem-sol.fif')
dip, _ = mne.fit_dipole(evoked, noise_cov, bem, trans)
dip.save(join(meg_dir, 'sample_audvis_set1.dip'))
bem = subjects_dir + '0001/bem/0001-inner_skull-bem-sol.fif'
# Note that forward solutions can also be read with read_forward_solution
fwd = mne.make_forward_solution(raw_fname, trans, src, bem,
fname="0001-fwd.fif", meg=True, eeg=False,
mindist=5.0,
n_jobs=n_jobs, overwrite=True)
# convert to surface orientation for better visualization
fwd = mne.convert_forward_solution(fwd, surf_ori=True)
leadfield = fwd['sol']['data']
print("Leadfield size : %d x %d" % leadfield.shape)
grad_map = mne.sensitivity_map(fwd, ch_type='grad', mode='fixed')
mag_map = mne.sensitivity_map(fwd, ch_type='mag', mode='fixed')
###############################################################################
# Show gain matrix a.k.a. leadfield matrix with sensitivity map
picks_meg = mne.pick_types(fwd['info'], meg=True, eeg=False)
fig, axes = plt.subplots(2, 1, figsize=(10, 8), sharex=True)
fig.suptitle('Lead field matrix (500 dipoles only)', fontsize=14)
for ax, picks, ch_type in zip(axes, [picks_meg], ['meg']):
im = ax.imshow(leadfield[picks, :], origin='lower', aspect='auto',
cmap='RdBu_r')
ax.set_title(ch_type.upper())
ax.set_xlabel('sources')
ax.set_ylabel('sensors')
# Then we can compute the forward solution.
info = hcp.read_info(subject=subject,
hcp_path=hcp_path,
data_type='rest',
run_index=0)
picks = mne.pick_types(info, meg=True, ref_meg=False)
info = mne.pick_info(info, picks)
fwd = mne.make_forward_solution(info,
trans=head_mri_t,
bem=bem_sol,
src=src_subject)
mag_map = mne.sensitivity_map(fwd,
projs=None,
ch_type='mag',
mode='fixed',
exclude=[],
verbose=None)
##############################################################################
# we display sensitivity map on the original surface with little smoothing
# and admire the expected curvature-driven sensitivity pattern.
mag_map = mag_map.to_original_src(src_fsaverage, subjects_dir=subjects_dir)
mag_map.plot(subject='fsaverage',
subjects_dir=subjects_dir,
clim=dict(kind='percent', lims=[0, 50, 99]),
smoothing_steps=2)
def run():
args = sys.argv
if len(args) <= 1:
print 'Usage: run_meg_tutorial.sh <sample data directory>'
return
sample_dir = args[1]
subjects_dir = join(sample_dir, 'subjects')
meg_dir = join(sample_dir, 'MEG', 'sample')
os.environ['SUBJECTS_DIR'] = subjects_dir
os.environ['MEG_DIR'] = meg_dir
subject = 'sample'
src = setup_source_space(subject, fname=True, spacing='oct6', n_jobs=2,
overwrite=True)
# If one wanted to use other source spaces, these types of options are
# available
src_fsaverage = setup_source_space('fsaverage', fname=True, spacing='ico5',
n_jobs=2, overwrite=True,
add_dist=False)
morph_source_spaces(src_fsaverage, subject_to='sample')
setup_source_space(subject, fname=True, spacing='all', overwrite=True,
n_jobs=2, add_dist=False)
# Add distances to source space (if desired, takes a long time)
bem_dir = join(subjects_dir, join('sample', 'bem'))
os.rename(join(bem_dir, 'sample-oct-6-src.fif'),
join(bem_dir, 'sample-oct-6-orig-src.fif'))
new_src = add_source_space_distances(src, dist_limit=0.007)
new_src.save(join(bem_dir, 'sample-oct-6-src.fif'))
# Preprocessing
raw = mne.io.Raw(join(meg_dir, 'sample_audvis_raw.fif'), preload=True)
raw.info['bads'] = ['MEG 2443', 'EEG 053']
reject = dict(grad=3000e-13, mag=4000e-15, eeg=100e-6)
ecg_proj, _ = mne.preprocessing.compute_proj_ecg(raw, l_freq=1, h_freq=100,
ch_name='MEG 1531',
reject=reject)
eog_proj, _ = mne.preprocessing.compute_proj_eog(raw, l_freq=1, h_freq=35,
reject=reject,
no_proj=True)
events = mne.find_events(raw)
mne.write_events(join(meg_dir, 'sample_audvis_raw-eve.fif'), events)
event_id = [1, 2, 3, 4]
tmin, tmax = -0.2, 0.5
picks = mne.pick_types(raw.info, meg=True, eeg=True, stim=True, eog=True)
# Average with no filter
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks)
evoked = epochs.average()
evoked.save(join(meg_dir, 'sample_audvis-no-filter-ave.fif'))
raw.filter(l_freq=None, h_freq=40)
raw_resampled = raw.resample(150)
raw_resampled.save(join(meg_dir, 'sample_audvis_filt-0-40_raw.fif'),
overwrite=True)
raw.add_proj(ecg_proj)
raw.add_proj(eog_proj)
resampled_events = mne.find_events(raw_resampled)
mne.write_events(join(meg_dir, 'sample_audvis_filt-0-40_raw-eve.fif'),
resampled_events)
# Average with filter
epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks)
evoked = epochs.average()
evoked.save(join(meg_dir, 'sample_audvis-ave.fif'))
# Compute the noise covariance matrix
noise_cov = mne.compute_raw_data_covariance(raw, picks=picks)
noise_cov.save(join(meg_dir, 'audvis.cov'))
# Compute the empty-room noise covariance matrix
ernoise_raw = mne.io.Raw(join(meg_dir, 'ernoise_raw.fif'), preload=True)
ernoise_raw.info['bads'] = ['MEG 2443']
ernoise_raw.filter(l_freq=None, h_freq=40)
picks = mne.pick_types(ernoise_raw.info, meg=True, eeg=True, stim=True,
eog=True)
ernoise_cov = mne.compute_raw_data_covariance(ernoise_raw, picks=picks)
ernoise_cov.save(join(meg_dir, 'ernoise.cov'))
###############################################################################
# Compute forward solution a.k.a. lead field
trans = join(meg_dir, 'sample_audvis_raw-trans.fif')
bem = join(subjects_dir, 'sample', 'bem', 'sample-5120-bem-sol.fif')
# for MEG only
fname = join(meg_dir, 'sample_audvis-meg-oct-6-fwd.fif')
fwd_meg = mne.make_forward_solution(raw.info, trans, src, bem,
fname=fname, meg=True, eeg=False,
mindist=5.0, n_jobs=2, overwrite=True)
# for EEG only
bem = join(subjects_dir, 'sample', 'bem',
'sample-5120-5120-5120-bem-sol.fif')
fname = join(meg_dir, 'sample_audvis-eeg-oct-6-fwd.fif')
fwd_eeg = mne.make_forward_solution(raw.info, trans, src, bem,
fname=fname, meg=False, eeg=True,
mindist=5.0, n_jobs=2, overwrite=True)
# for both EEG and MEG
fname = join(meg_dir, 'sample_audvis-meg-eeg-oct-6-fwd.fif')
fwd = mne.make_forward_solution(raw.info, trans, src, bem,
fname=fname, meg=True, eeg=True,
mindist=5.0, n_jobs=2, overwrite=True)
# Create various sensitivity maps
grad_map = mne.sensitivity_map(fwd, ch_type='grad', mode='free')
grad_map.save(join(meg_dir, 'sample_audvis-grad-oct-6-fwd-sensmap'),
ftype='w')
mag_map = mne.sensitivity_map(fwd, ch_type='mag', mode='free')
mag_map.save(join(meg_dir, 'sample_audvis-mag-oct-6-fwd-sensmap'),
ftype='w')
eeg_map = mne.sensitivity_map(fwd, ch_type='eeg', mode='free')
eeg_map.save(join(meg_dir, 'sample_audvis-eeg-oct-6-fwd-sensmap'),
ftype='w')
grad_map2 = mne.sensitivity_map(fwd, ch_type='grad', mode='fixed')
grad_map2.save(join(meg_dir, 'sample_audvis-grad-oct-6-fwd-sensmap-2'),
ftype='w')
mag_map2 = mne.sensitivity_map(fwd, ch_type='mag', mode='ratio')
mag_map2.save(join(meg_dir, 'sample_audvis-mag-oct-6-fwd-sensmap-3'),
ftype='w')
# Compute some with the EOG + ECG projectors
projs = ecg_proj + eog_proj + raw.info['projs']
for map_type in ['radiality', 'angle', 'remaining', 'dampening']:
eeg_map = mne.sensitivity_map(fwd, projs=projs, ch_type='eeg',
mode=map_type)
eeg_map.save(join(meg_dir,
'sample_audvis-eeg-oct-6-fwd-sensmap-' + map_type))
###############################################################################
# Compute MNE inverse operators
#
# Note: The MEG/EEG forward solution could be used for all
#
inv_meg = make_inverse_operator(raw.info, fwd_meg, noise_cov, loose=0.2)
fname = join(meg_dir, 'sample_audvis-meg-oct-6-meg-inv.fif')
write_inverse_operator(fname, inv_meg)
inv_eeg = make_inverse_operator(raw.info, fwd_eeg, noise_cov, loose=0.2)
fname = join(meg_dir, 'sample_audvis-eeg-oct-6-eeg-inv.fif')
write_inverse_operator(fname, inv_eeg)
inv = make_inverse_operator(raw.info, fwd, noise_cov, loose=0.2)
fname = join(meg_dir, 'sample_audvis-meg-eeg-oct-6-meg-eeg-inv.fif')
write_inverse_operator(fname, inv)
# inverse operator with fixed orientation (for testing). Not implemented
#inv_fixed = make_inverse_operator(raw.info, fwd_meg, noise_cov,
# depth=None, fixed=True)
#fname = join(meg_dir, 'sample_audvis-meg-oct-6-meg-nodepth-fixed-inv.fif')
#write_inverse_operator(fname, inv_fixed)
# produce two with diagonal noise (for testing)
diag = noise_cov.as_diag()
inv_meg_diag = make_inverse_operator(raw.info, fwd_meg, diag, loose=0.2)
fname = join(meg_dir, 'sample_audvis-meg-oct-6-meg-diagnoise-inv.fif')
write_inverse_operator(fname, inv_meg_diag)
inv_eeg_diag = make_inverse_operator(raw.info, fwd, diag, loose=0.2)
fname = join(meg_dir,
'sample_audvis-meg-eeg-oct-6-meg-eeg-diagnoise-inv.fif')
write_inverse_operator(fname, inv_eeg_diag)
# Produce stc files
evoked.crop(0, 0.25)
stc_meg = apply_inverse(evoked, inv_meg, method='MNE')
stc_meg.save(join(meg_dir, 'sample_audvis-meg'))
stc_eeg = apply_inverse(evoked, inv_eeg, method='MNE')
stc_eeg.save(join(meg_dir, 'sample_audvis-eeg'))
stc = apply_inverse(evoked, inv, method='MNE')
stc.save(join(meg_dir, 'sample_audvis-meg-eeg'))
# let's also morph to fsaverage
stc_to = stc_meg.morph('fsaverage', grade=3, smooth=12)
stc_to.save(join(meg_dir, 'fsaverage_audvis-meg'))
stc_to = stc_eeg.morph('fsaverage', grade=3, smooth=12)
stc_to.save(join(meg_dir, 'fsaverage_audvis-eeg'))
stc_to = stc.morph('fsaverage', grade=3, smooth=12)
stc_to.save(join(meg_dir, 'fsaverage_audvis-meg-eeg'))
###############################################################################
# Do one dipole fitting
evoked = evoked.pick_types(meg=True, eeg=False)
evoked.crop(0.04, 0.095)
bem = join(subjects_dir, 'sample', 'bem', 'sample-5120-bem-sol.fif')
dip, _ = mne.fit_dipole(evoked, noise_cov, bem, trans)
dip.save(join(meg_dir, 'sample_audvis_set1.dip'))
import matplotlib.pyplot as plt
from mne import read_forward_solution, read_proj, sensitivity_map
from mne.datasets import sample
print(__doc__)
data_path = sample.data_path()
subjects_dir = data_path + '/subjects'
fname = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif'
ecg_fname = data_path + '/MEG/sample/sample_audvis_ecg-proj.fif'
fwd = read_forward_solution(fname, surf_ori=True)
projs = read_proj(ecg_fname)
projs = projs[3:][::2] # take only one projection per channel type
# Compute sensitivity map
ssp_ecg_map = sensitivity_map(fwd, ch_type='grad', projs=projs, mode='angle')
###############################################################################
# Show sensitivity map
plt.hist(ssp_ecg_map.data.ravel())
plt.show()
args = dict(clim=dict(kind='value', lims=(0.2, 0.6, 1.)), smoothing_steps=7,
hemi='rh', subjects_dir=subjects_dir)
ssp_ecg_map.plot(subject='sample', time_label='ECG SSP sensitivity', **args)
eeg=False, # exclude EEG channels
mindist=5.0, # ignore sources <= 5mm from inner skull
n_jobs=1) # number of jobs to run in parallel
mne.write_forward_solution(fwd_fname, fwd, overwrite=True)
if operations_to_apply['LeadfieldMatrix']:
fwd = mne.convert_forward_solution(fwd, surf_ori=True)
leadfield = fwd['sol']['data']
print(
"Leadfield size : %d sensors x %d dipoles" %
leadfield.shape) ## three times the number of vertices -- x, y, z
# Compute sensitivity maps for gradiometers
sens_map = mne.sensitivity_map(fwd,
ch_type=str(SensorType),
mode='fixed')
# # Show gain matrix a.k.a. leadfield matrix with sensitivy map
picks = mne.pick_types(fwd['info'], meg=str(SensorType), eeg=False)
im = plt.imshow(leadfield[picks, :500],
origin='lower',
aspect='auto',
cmap='RdBu_r')
plt.xlabel('sources')
plt.ylabel('sensors')
plt.title('Lead field matrix for Gradiometers', fontsize=14)
plt.colorbar(cmap='RdBu_r')
plt.figure()
# Get relevant channel information
info = mne.io.read_info(raw_fname)
info = mne.pick_info(info, mne.pick_types(info, meg=True, eeg=False,
exclude=[]))
# Morph fsaverage's source space to sample
src_fs = mne.read_source_spaces(fname_src_fs)
src_morph = mne.morph_source_spaces(src_fs, subject_to='sample',
subjects_dir=subjects_dir)
# Compute the forward with our morphed source space
fwd = mne.make_forward_solution(info, trans=fname_trans,
src=src_morph, bem=fname_bem)
# fwd = mne.convert_forward_solution(fwd, surf_ori=True, force_fixed=True)
mag_map = mne.sensitivity_map(fwd, ch_type='mag')
# Return this SourceEstimate (on sample's surfaces) to fsaverage's surfaces
mag_map_fs = mag_map.to_original_src(src_fs, subjects_dir=subjects_dir)
# Plot the result, which tracks the sulcal-gyral folding
# outliers may occur, we'll place the cutoff at 99 percent.
kwargs = dict(clim=dict(kind='percent', lims=[0, 50, 99]),
# no smoothing, let's see the dipoles on the cortex.
smoothing_steps=1, hemi='rh', views=['lat'])
# Now note that the dipoles on fsaverage are almost equidistant while
# morphing will distribute the dipoles unevenly across the given subject's
# cortical surface to achieve the closest approximation to the average brain.
# Our testing code suggests a correlation of higher than 0.99.
raw_fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw.fif')
# Get relevant channel information
info = mne.io.read_info(raw_fname)
info = mne.pick_info(info, mne.pick_types(info, meg=True, eeg=False,
exclude=[]))
# Morph fsaverage's source space to sample
src_fs = mne.read_source_spaces(fname_src_fs)
src_morph = mne.morph_source_spaces(src_fs, subject_to='sample',
subjects_dir=subjects_dir)
# Compute the forward with our morphed source space
fwd = mne.make_forward_solution(info, trans=fname_trans,
src=src_morph, bem=fname_bem)
mag_map = mne.sensitivity_map(fwd, ch_type='mag')
# Return this SourceEstimate (on sample's surfaces) to fsaverage's surfaces
mag_map_fs = mag_map.to_original_src(src_fs, subjects_dir=subjects_dir)
# Plot the result, which tracks the sulcal-gyral folding
# outliers may occur, we'll place the cutoff at 99 percent.
kwargs = dict(clim=dict(kind='percent', lims=[0, 50, 99]),
# no smoothing, let's see the dipoles on the cortex.
smoothing_steps=1, hemi='rh', views=['lat'])
# Now note that the dipoles on fsaverage are almost equidistant while
# morphing will distribute the dipoles unevenly across the given subject's
# cortical surface to achieve the closest approximation to the average brain.
# Our testing code suggests a correlation of higher than 0.99.
src=src,
bem=bem,
fname=None,
meg=True,
eeg=True,
mindist=5.0,
n_jobs=2,
overwrite=True)
# convert to surface orientation for better visualization
fwd = mne.convert_forward_solution(fwd, surf_ori=True)
leadfield = fwd['sol']['data']
print("Leadfield size : %d x %d" % leadfield.shape)
grad_map = mne.sensitivity_map(fwd, ch_type='grad', mode='fixed')
mag_map = mne.sensitivity_map(fwd, ch_type='mag', mode='fixed')
eeg_map = mne.sensitivity_map(fwd, ch_type='eeg', mode='fixed')
###############################################################################
# Show gain matrix a.k.a. leadfield matrix with sensitivity map
picks_meg = mne.pick_types(fwd['info'], meg=True, eeg=False)
picks_eeg = mne.pick_types(fwd['info'], meg=False, eeg=True)
fig, axes = plt.subplots(2, 1, figsize=(10, 8), sharex=True)
fig.suptitle('Lead field matrix (500 dipoles only)', fontsize=14)
for ax, picks, ch_type in zip(axes, [picks_meg, picks_eeg], ['meg', 'eeg']):
im = ax.imshow(leadfield[picks, :500],
origin='lower',
aspect='auto',
print __doc__
import mne
from mne.datasets import sample
data_path = sample.data_path()
fname = data_path + "/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif"
subjects_dir = data_path + "/subjects"
fwd = mne.read_forward_solution(fname, surf_ori=True)
leadfield = fwd["sol"]["data"]
print "Leadfield size : %d x %d" % leadfield.shape
grad_map = mne.sensitivity_map(fwd, ch_type="grad", mode="fixed")
mag_map = mne.sensitivity_map(fwd, ch_type="mag", mode="fixed")
eeg_map = mne.sensitivity_map(fwd, ch_type="eeg", mode="fixed")
###############################################################################
# Show gain matrix a.k.a. leadfield matrix with sensitivy map
import pylab as pl
pl.matshow(leadfield[:, :500])
pl.xlabel("sources")
pl.ylabel("sensors")
pl.title("Lead field matrix (500 dipoles only)")
pl.figure()
pl.hist(
transform=True)
raw.set_montage(montage)
raw.set_eeg_reference(projection=True) # needed for inverse modeling
# Check that the locations of EEG electrodes is correct with respect to MRI
mne.viz.plot_alignment(raw.info,
src=src,
eeg=['original', 'projected'],
trans=trans,
dig=True)
##############################################################################
# Setup source space and compute forward
# --------------------------------------
fwd = mne.make_forward_solution(raw.info,
trans=trans,
src=src,
bem=bem,
eeg=True,
mindist=5.0,
n_jobs=1)
print(fwd)
# for illustration purposes use fwd to compute the sensitivity map
eeg_map = mne.sensitivity_map(fwd, ch_type='eeg', mode='fixed')
eeg_map.plot(time_label='EEG sensitivity',
subjects_dir=subjects_dir,
clim=dict(lims=[5, 50, 100]))
def run_evoked(subject_id):
subject = "sub%03d" % subject_id
print("processing subject: %s" % subject)
in_path = op.join(data_path, "EEG_Process")
evo_path = op.join(data_path, "EEG_Evoked")
for run in range(1, 2):
fname = op.join(in_path, 'sub_%03d_raw-epo.fif' % (subject_id, ))
epochs = mne.read_epochs(fname, preload=True)
#compute covariance for later on (inverse solution)
fname_cov = op.join(evo_path,
"sub_%03d_LSF_HSF-cov.fif" % (subject_id, ))
cv = KFold(3, random_state=97) # make sure cv is deterministic
cov = mne.compute_covariance(epochs,
tmax=-0.01,
method='shrunk',
cv=cv)
cov.save(fname_cov)
mne.viz.plot_cov(cov, epochs.info)
#general: HSF vs LSF
evoked_LSF = epochs['LSF'].average()
evoked_HSF = epochs['HSF'].average()
contrast = mne.combine_evoked([evoked_HSF, evoked_LSF],
weights=[1, -1])
#name the conditions
# Simplify comment
evoked_LSF.comment = 'evoked_LSF'
evoked_HSF.comment = 'evoked_HSF'
contrast.comment = 'contrast'
#contrast.plot(picks=('Oz'), window_title='CONTRAST')
#plot
#evoked_LSF.plot(picks=['Oz'], window_title='evoked, condition LSF, electrode Oz')
#evoked_HSF.plot(picks=['Oz'], window_title='evoked, condition HSF, electrode Oz')
fname_evo = op.join(evo_path,
"sub_%03d_LSF_HSF-ave.fif" % (subject_id, ))
mne.evoked.write_evokeds(fname_evo, [evoked_LSF, evoked_HSF, contrast])
#compute forward solution for later on (inverse solution)
fname_fwd = op.join(evo_path,
"sub_%03d_LSF_HSF-fwd.fif" % (subject_id, ))
info = mne.io.read_info(fname_evo)
fwd = mne.make_forward_solution(info=info,
trans=trans,
src=src,
bem=bem,
eeg=True,
mindist=5.0,
n_jobs=1)
print(fwd)
leadfield = fwd['sol']['data']
print("Leadfield size : %d sensors x %d dipoles" % leadfield.shape)
mne.write_forward_solution(fname_fwd, fwd, overwrite=True)
# for illustration purposes use fwd to compute the sensitivity map
eeg_map = mne.sensitivity_map(fwd, ch_type='eeg', mode='fixed')
eeg_map.plot(time_label='EEG sensitivity LSF',
clim=dict(lims=[5, 50, 100]))
