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')