#
# We need a matching forward solution and inverse operator to compute
# resolution matrices for different methods.
data_path = sample.data_path()
subjects_dir = data_path + '/subjects'
fname_fwd = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif'
fname_inv = data_path + '/MEG/sample/sample_audvis-meg-oct-6-meg-fixed-inv.fif'
forward = mne.read_forward_solution(fname_fwd)
# Convert forward solution to fixed source orientations
mne.convert_forward_solution(
forward, surf_ori=True, force_fixed=True, copy=False)
inverse_operator = read_inverse_operator(fname_inv)
# Compute resolution matrices for MNE
rm_mne = make_inverse_resolution_matrix(forward, inverse_operator,
method='MNE', lambda2=1. / 3.**2)
src = inverse_operator['src']
del forward, inverse_operator # save memory
# %%
# Read and organise labels for cortical parcellation
# --------------------------------------------------
#
# Get labels for FreeSurfer 'aparc' cortical parcellation with 34 labels/hemi
labels = mne.read_labels_from_annot('sample', parc='aparc',
subjects_dir=subjects_dir)
n_labels = len(labels)
label_colors = [label.color for label in labels]
# First, we reorder the labels based on their location in the left hemi
label_names = [label.name for label in labels]
lh_labels = [name for name in label_names if name.endswith('lh')]
# make inverse operator from forward solution
# free source orientation
inverse_operator = mne.minimum_norm.make_inverse_operator(info=evoked.info,
forward=forward,
noise_cov=noise_cov,
loose=0.,
depth=None)
# regularisation parameter
snr = 3.0
lambda2 = 1.0 / snr**2
method = 'MNE' # can be 'MNE' or 'sLORETA'
# compute resolution matrix for sLORETA
rm_lor = make_inverse_resolution_matrix(forward,
inverse_operator,
method='sLORETA',
lambda2=lambda2)
# get PSF and CTF for sLORETA at one vertex
sources = [1000]
stc_psf = get_point_spread(rm_lor, forward['src'], sources, norm=True)
stc_ctf = get_cross_talk(rm_lor, forward['src'], sources, norm=True)
del rm_lor
##############################################################################
# Visualize
# ---------
# PSF:
noise_cov=noise_cov,
loose=0.,
depth=None)
# regularisation parameter
snr = 3.0
lambda2 = 1.0 / snr**2
# %%
# MNE
# ---
# Compute resolution matrices, peak localisation error (PLE) for point spread
# functions (PSFs), spatial deviation (SD) for PSFs:
rm_mne = make_inverse_resolution_matrix(forward,
inverse_operator,
method='MNE',
lambda2=lambda2)
ple_mne_psf = resolution_metrics(rm_mne,
inverse_operator['src'],
function='psf',
metric='peak_err')
sd_mne_psf = resolution_metrics(rm_mne,
inverse_operator['src'],
function='psf',
metric='sd_ext')
del rm_mne
# %%
# dSPM
# ----
# Do the same for dSPM:
# Read forward solution
forward = mne.read_forward_solution(fname_fwd)
# Convert to fixed source orientations
forward = mne.convert_forward_solution(forward,
surf_ori=True,
force_fixed=True)
# Read inverse operator
inverse_operator = read_inverse_operator(fname_inv)
# Compute resolution matrices for MNE and sLORETA
lambda2 = 1. / 3.**2
method = 'MNE'
rm_mne = make_inverse_resolution_matrix(forward,
inverse_operator,
method=method,
lambda2=lambda2)
method = 'sLORETA'
rm_lor = make_inverse_resolution_matrix(forward,
inverse_operator,
method=method,
lambda2=lambda2)
###############################################################################
# Read and organise labels for cortical parcellation
# --------------------------------------------------
#
# Get labels for FreeSurfer 'aparc' cortical parcellation with 34 labels/hemi
labels = mne.read_labels_from_annot('sample',
parc='aparc',
subjects_dir=subjects_dir)
meth_str = '%s_%s' % ('LCMV', cov_lat_str)
functions_and_metrics(resmat, fwd_use['src'], functions,
metrics, subject, meth_str)
# Save some PSFs
filetext = meth_str + '_PSFs'
fname = fname_stc = C.fname_STC(C, C.resolution_subdir,
subject, filetext)
save_resolution_matrix(fname, resmat, invop['src'], gap=10)
else: # for MNE-type estimators
# Compute resolution matrix
resmat = make_inverse_resolution_matrix(fwd_use,
invop,
method=method,
lambda2=lambda2)
functions_and_metrics(resmat, fwd_use['src'], functions,
metrics, subject, meth_name)
# Save some PSFs
filetext = meth_name + '_PSFs'
fname = fname_stc = C.fname_STC(C, C.resolution_subdir,
subject, filetext)
save_resolution_matrix(fname, resmat, invop['src'], gap=10)
raw_fname = data_path + meg + 'block_SD_tsss_raw.fif'
info = mne.io.read_info(raw_fname)
# make an inverse operator
inv_op = make_inverse_operator(info, fwd, noise_cov=cov,
fixed=True, loose=0., depth=None,
verbose=None)
# # Reading inverse operator (from one task)
# inv_fname = data_path + meg + inv_op_name[0]
# inv_op = read_inverse_operator(inv_fname)
# Compute resolution matrix for MNE
lambda2 = 1. / 3.**2
method = 'MNE'
rm = make_inverse_resolution_matrix(fwd, inv_op, method=method,
lambda2=lambda2)
# Source space used for inverse operator
src = inv_op['src']
# Compute first SVD component across PSFs within labels
# Note the differences in explained variance, probably due to different
# spatial extents of labels
n_comp = 5
stcs_psf, pca_vars = get_point_spread(
rm, src, labels, mode='pca', n_comp=n_comp, norm=None,
return_pca_vars=True)
morph = mne.compute_source_morph( src=inv_op['src'], subject_from\
= stcs_psf[0].subject , subject_to = C.subject_to , spacing = \