def plot_noise_covariance(name, save_dir, lowpass, subject, save_plots,
figures_path):
noise_covariance = io.read_noise_covariance(name, save_dir, lowpass)
info = io.read_info(name, save_dir)
fig_cov = noise_covariance.plot(info, show_svd=False)
if save_plots:
save_path = join(figures_path, subject, 'noise_covariance', name + \
filter_string(lowpass) + '.jpg')
fig_cov[0].savefig(save_path, dpi=600)
print 'figure: ' + save_path + ' has been saved'
else:
print 'Not saving plots; set "save_plots" to "True" to save'
def plot_transformation(name, save_dir, subject, subjects_dir, save_plots,
figures_path):
info = io.read_info(name, save_dir)
trans = io.read_transformation(name, save_dir)
mne.viz.plot_alignment(info, trans, subject, subjects_dir,
surfaces=['head-dense', 'inner_skull', 'brain'])#,
# skull=['inner_skull', 'outer_skull'],
# brain=True)
mayavi.mlab.view(0, -90)
if save_plots:
save_path = join(figures_path, subject, 'transformation', name + \
'.jpg')
mayavi.mlab.savefig(save_path)
print 'figure: ' + save_path + ' has been saved'
else:
print 'Not saving plots; set "save_plots" to "True" to save'
def create_inverse_operator(name, save_dir, lowpass, overwrite):
inverse_operator_name = name + filter_string(lowpass) + '-inv.fif'
inverse_operator_path = join(save_dir, inverse_operator_name)
if overwrite or not isfile(inverse_operator_path):
info = io.read_info(name, save_dir)
noise_covariance = io.read_noise_covariance(name, save_dir, lowpass)
forward = io.read_forward(name, save_dir)
inverse_operator = mne.minimum_norm.make_inverse_operator(
info, forward, noise_covariance)
mne.minimum_norm.write_inverse_operator(inverse_operator_path,
inverse_operator)
else:
print('inverse operator file: '+ inverse_operator_path + \
' already exists')
def create_forward_solution(name, save_dir, subject, subjects_dir,
overwrite):
forward_name = name + '-fwd.fif'
forward_path = join(save_dir, forward_name)
if overwrite or not isfile(forward_path):
info = io.read_info(name, save_dir)
trans = io.read_transformation(name, save_dir)
bem = io.read_bem_solution(subject, subjects_dir)
source_space = io.read_source_space(subject, subjects_dir)
forward = mne.make_forward_solution(info, trans, source_space, bem,
n_jobs=1)
mne.write_forward_solution(forward_path, forward, overwrite)
else:
print('forward solution: ' + forward_path + ' already exists')