Index

A

add_center() (in module pynibs.util.utils) add_experiment_info() (pynibs.subject.Subject method) add_mesh_info() (pynibs.subject.Subject method) add_mri_info() (pynibs.subject.Subject method) add_plotsettings() (pynibs.subject.Subject method)

add_roi_info() (pynibs.subject.Subject method) add_sigmoidal_bestfit() (in module pynibs.expio.exp) arrays_similar() (in module pynibs.expio.localite) assign_found_hotspot_single() (in module pynibs.regression.dual_node_detection) assign_found_hotspots() (in module pynibs.regression.dual_node_detection)

B

bases2rotmat() (in module pynibs.util.rotations) bash() (in module pynibs.util.utils) bash_call() (in module pynibs.util.utils) binarize_real_meps() (in module pynibs.regression.dual_node_detection) binarize_response_data() (in module pynibs.regression.dual_node_detection) biphasic_pulse() (in module pynibs.tms_pulse)

BrainsightCSVParser (class in pynibs.expio.brainsight) BrainsightCSVParser.State (class in pynibs.expio.brainsight) butter_highpass() (in module pynibs.expio.Mep) butter_highpass_filter() (in module pynibs.expio.Mep) butter_lowpass() (in module pynibs.expio.Mep) butter_lowpass_filter() (in module pynibs.expio.Mep)

C

c_map_comparison() (in module pynibs.util.quality_measures) calc_coil_position_pdf() (in module pynibs.coil.coil) calc_coil_transformation_matrix() (in module pynibs.coil.coil) calc_dist_pairwise() (in module pynibs.regression.dual_node_detection) calc_distances() (in module pynibs.mesh.utils) calc_e() (in module pynibs.optimization.multichannel) calc_E() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_e_effective() (in module pynibs.neuron.neuron_regression) calc_E_normal_tangential_surface() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_E_on_GM_WM_surface() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_E_on_GM_WM_surface3() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_E_on_GM_WM_surface_simnibs() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_E_on_GM_WM_surface_simnibs_KW() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_e_threshold() (in module pynibs.neuron.neuron_regression) calc_emg_preactivation() (in module pynibs.expio.Mep) calc_gradient() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_gradient_surface() (in module pynibs.mesh.utils) calc_J() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_ll() (in module pynibs.optimization.multichannel) calc_mep_wilson() (in module pynibs.muap) calc_motor_threshold() (pynibs.expio.Mep.Mep method) calc_n_network_combs() (in module pynibs.util.utils) calc_opt_gain_map() (in module pynibs.optimization.coil_opt) calc_outlier() (in module pynibs.expio.exp) calc_p2p() (in module pynibs.expio.Mep) calc_p2p_old_exp0() (in module pynibs.expio.Mep) calc_p2p_old_exp1() (in module pynibs.expio.Mep) calc_q_coupling_model() (in module pynibs.neuron.neuron_regression) calc_QOI_in_points() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_QOI_in_points_tet_idx() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_score() (pynibs.regression.regression.Element method) calc_surface_adjacent_tetrahedra_idx_list() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_tet_volume() (in module pynibs.mesh.utils) calc_tetrahedra_volume_cross() (in module pynibs.mesh.utils) calc_tetrahedra_volume_det() (in module pynibs.mesh.utils) calc_tms_motion_params() (in module pynibs.util.quality_measures) calc_tri_surface() (in module pynibs.mesh.utils) calculate_strain() (in module pynibs.optimization.multichannel) calculate_triangle_area() (in module pynibs.optimization.multichannel) cell_data_to_point_data() (in module pynibs.mesh.transformations) cell_data_to_point_data_vtk() (in module pynibs.mesh.transformations) center (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) cf_curveshift_kernel() (in module pynibs.congruence.congruence) cf_curveshift_workhorse() (in module pynibs.congruence.congruence) cf_curveshift_workhorse_stretch_correction() (in module pynibs.congruence.congruence) cf_curveshift_workhorse_stretch_correction_new() (in module pynibs.congruence.congruence) cf_curveshift_workhorse_stretch_correction_sign_new() (in module pynibs.congruence.congruence) cf_curveshift_workhorse_stretch_correction_variance() (in module pynibs.congruence.congruence) cf_variance_sign_workhorse() (in module pynibs.congruence.congruence) cf_variance_workhorse() (in module pynibs.congruence.congruence) cfs2hdf5() (in module pynibs.expio.signal_ced)

check_coil_position() (in module pynibs.coil.coil) check_file_and_format() (in module pynibs.subject) check_islands_for_single_elm() (in module pynibs.mesh.utils) check_state_transition() (pynibs.expio.brainsight.BrainsightCSVParser method), [1] clean_roi() (in module pynibs.roi.roi_utils) coil_distance_correction() (in module pynibs.expio.exp) coil_distance_correction_matsimnibs() (in module pynibs.expio.exp) coil_outlier_correction_cond() (in module pynibs.expio.exp) coil_wise_corr() (in module pynibs.optimization.workhorses) combine_nnav_ft() (in module pynibs.expio.localite) combine_nnav_mep() (in module pynibs.expio.localite) combine_nnav_rt() (in module pynibs.expio.localite) compute_chunks() (in module pynibs.util.utils) compute_correlation_with_all_elements() (in module pynibs.regression.dual_node_detection) compute_pcd() (in module pynibs.util.quality_measures) compute_scores_with_all_elements() (in module pynibs.regression.dual_node_detection) compute_scores_with_all_elements_MP() (in module pynibs.regression.dual_node_detection) compute_scores_with_single_element_clf() (in module pynibs.regression.dual_node_detection) compute_scores_with_single_element_regression() (in module pynibs.regression.dual_node_detection) compute_signal() (in module pynibs.muap) constraint_min_current() (in module pynibs.optimization.multichannel) convert_csv_to_hdf5() (in module pynibs.expio.exp) copt (pynibs.expio.Mep.Mep attribute) cortical_depth() (in module pynibs.mesh.utils) CorticalLayer (class in pynibs.roi.roi_structs) CorticalLayer.Settings (class in pynibs.roi.roi_structs) coverage() (in module pynibs.optimization.workhorses) coverage_prepare() (in module pynibs.optimization.workhorses) create_electrode() (in module pynibs.muap) create_fibre_geo_hdf5() (in module pynibs.hdf5_io.hdf5_io) create_fibre_xdmf() (in module pynibs.hdf5_io.xdmf) create_in_bbox() (pynibs.roi.roi_structs.CorticalLayer class method) create_in_roi() (pynibs.roi.roi_structs.CorticalLayer class method) create_merged_nnav_emg_file_brainsight() (in module pynibs.expio.brainsight) create_muscle_coords() (in module pynibs.muap) create_muscle_fibre() (in module pynibs.muap) create_plot_settings_dict() (in module pynibs.subject) create_refine_spherical_roi() (in module pynibs.roi.roi_utils) create_response_data() (in module pynibs.regression.dual_node_detection) create_sensor_matrix() (in module pynibs.muap) create_signal_matrix() (in module pynibs.muap) create_stimsite_from_exp_hdf5() (in module pynibs.coil.export) create_stimsite_from_list() (in module pynibs.coil.export) create_stimsite_from_matsimnibs() (in module pynibs.coil.export) create_stimsite_from_tmslist() (in module pynibs.coil.export) create_stimsite_hdf5() (in module pynibs.coil.export) crop_mesh_with_box() (pynibs.roi.roi_structs.CorticalLayer static method) crop_mesh_with_surface() (pynibs.roi.roi_structs.CorticalLayer static method) cross_product() (in module pynibs.util.utils) cross_product_einsum2() (in module pynibs.util.utils) current_state (pynibs.expio.brainsight.BrainsightCSVParser attribute)

D

data (pynibs.expio.brainsight.BrainsightCSVParser attribute) DATA (pynibs.expio.brainsight.BrainsightCSVParser.State attribute) data_elements2nodes() (in module pynibs.mesh.transformations) (pynibs.mesh.mesh_struct.TetrahedraLinear method) DATA_HEADER (pynibs.expio.brainsight.BrainsightCSVParser.State attribute) data_nodes2elements() (in module pynibs.mesh.transformations) (pynibs.mesh.mesh_struct.TetrahedraLinear method) data_sub2avg() (in module pynibs.freesurfer) data_superimpose() (in module pynibs.hdf5_io.xdmf) decimate() (pynibs.roi.roi_structs.RegionOfInterestSurface method) delta (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) determine_coil_position_idcs() (in module pynibs.regression.dual_node_detection) determine_detectable_hotspots() (in module pynibs.regression.dual_node_detection)

determine_e_midlayer() (in module pynibs.mesh.utils) determine_e_midlayer_workhorse() (in module pynibs.mesh.utils) determine_element_idx_in_mesh() (in module pynibs.roi.roi_utils) (pynibs.roi.roi_structs.RegionOfInterestSurface method) determine_scoring_idcs() (in module pynibs.regression.dual_node_detection) DI_wave() (in module pynibs.neuron.util) differential_evolution() (in module pynibs.util.utils) dipole_potential() (in module pynibs.muap) dist() (in module pynibs.optimization.workhorses) dist_mc() (in module pynibs.optimization.workhorses) dist_svd() (in module pynibs.optimization.workhorses) doptimal_select() (in module pynibs.optimization.coil_sampling) dummy_fun() (in module pynibs.expio.fit_funs) dvs_likelihood() (in module pynibs.congruence.ext_metrics)

E

e_cog_workhorse() (in module pynibs.congruence.ext_metrics) e_focal_workhorse() (in module pynibs.congruence.ext_metrics) elem_workhorse() (in module pynibs.roi.roi_utils) Element (class in pynibs.regression.regression) ellipse_eccentricity() (in module pynibs.tensor_scaling) euclidean_dist() (in module pynibs.util.quality_measures) euler_angles_to_rotation_matrix() (in module pynibs.util.rotations) eval() (pynibs.expio.Mep.Mep method)

eval_fun_sig() (pynibs.expio.Mep.Mep method) eval_opt() (pynibs.expio.Mep.Mep method) eval_uncertainties() (pynibs.expio.Mep.Mep method) evaluate_network_identification() (in module pynibs.regression.dual_node_detection) exp() (in module pynibs.expio.fit_funs) exp0() (in module pynibs.expio.fit_funs) exp0_log() (in module pynibs.expio.fit_funs) exp_log() (in module pynibs.expio.fit_funs) extract_condition_combination() (in module pynibs.congruence.congruence)

F

FILE_HEADER (pynibs.expio.brainsight.BrainsightCSVParser.State attribute) fill_defaults() (pynibs.mesh.mesh_struct.Mesh method) fill_from_dict() (in module pynibs.subject) filter_emg() (in module pynibs.expio.visor) fim() (in module pynibs.optimization.workhorses) fim_mc() (in module pynibs.optimization.workhorses) fim_svd() (in module pynibs.optimization.workhorses) FIN (pynibs.expio.brainsight.BrainsightCSVParser.State attribute) find_distinct_hotspots() (in module pynibs.regression.dual_node_detection) find_distinct_single_hotspot() (in module pynibs.regression.dual_node_detection) find_element_idx_by_points() (in module pynibs.mesh.utils) find_island_elms() (in module pynibs.mesh.utils) find_islands() (in module pynibs.mesh.utils) find_nearest() (in module pynibs.mesh.utils)

fit (pynibs.expio.Mep.Mep attribute) fit_elms() (in module pynibs.regression.regression) fit_mep_to_function() (pynibs.expio.Mep.Mep method) fit_mep_to_function_multistart() (pynibs.expio.Mep.Mep method) fn_mask (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) fn_mask_avg (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) fn_mask_nii (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) foc_opt() (in module pynibs.optimization.multichannel) foc_opt_worker_fun() (in module pynibs.optimization.multichannel) foc_targets() (in module pynibs.optimization.multichannel) fps_select() (in module pynibs.optimization.coil_sampling) freesurfer2vtk() (in module pynibs.freesurfer) fun (pynibs.expio.Mep.Mep attribute) fun_sig (pynibs.expio.Mep.Mep attribute)

G

generalized_extreme_value_distribution() (in module pynibs.util.utils) generate_cortical_laminae() (pynibs.roi.roi_structs.RegionOfInterestSurface method) generate_layer() (pynibs.roi.roi_structs.CorticalLayer method) geodesic_dist() (in module pynibs.util.quality_measures) get_bad_elms() (in module pynibs.regression.regression) get_cartesian_product() (in module pynibs.util.utils) get_cnt_data() (in module pynibs.expio.visor) get_cnt_infos() (in module pynibs.expio.exp) get_coil_dipole_pos() (in module pynibs.coil.coil) get_coil_flip_m() (in module pynibs.expio.exp) get_coil_sn_lst() (in module pynibs.expio.exp) get_csv_matrix() (in module pynibs.expio.exp) get_current_init() (in module pynibs.optimization.multichannel) get_det_fim() (in module pynibs.optimization.opt_mep) get_evenly_spaced_element_subset() (pynibs.roi.roi_structs.CorticalLayer method) get_faces() (pynibs.mesh.mesh_struct.TetrahedraLinear method) get_fim_sample() (in module pynibs.optimization.opt_mep) get_focality_score() (in module pynibs.optimization.multichannel) get_ft_data_from_csv() (in module pynibs.expio.exp) get_indices_discontinuous_data() (in module pynibs.mesh.utils) get_instrument_marker() (in module pynibs.expio.visor) get_intensity_e() (in module pynibs.util.dosing) get_intensity_e_old() (in module pynibs.util.dosing) get_intensity_stokes() (in module pynibs.util.dosing) get_invalid_coil_parameters() (in module pynibs.coil.coil) get_marker() (in module pynibs.expio.brainsight) (in module pynibs.expio.localite)

get_mask() (in module pynibs.roi.roi_utils) get_maximality_currents() (in module pynibs.optimization.multichannel) get_mep_elements() (in module pynibs.expio) (in module pynibs.expio.neurone) (in module pynibs.expio.signal_ced) get_mep_sampling_rate() (in module pynibs.expio.Mep) get_mep_virtual_subject_DVS() (in module pynibs.expio.Mep) get_mep_virtual_subject_TVS() (in module pynibs.expio.Mep) get_model_init_values() (in module pynibs.regression.regression) get_optimal_coil_positions() (in module pynibs.optimization.coil_opt) get_optimal_sample_fim() (in module pynibs.optimization.opt_mep) get_outside_faces() (pynibs.mesh.mesh_struct.TetrahedraLinear method) get_patient_id() (in module pynibs.expio.localite) get_quadrant_samples() (in module pynibs.regression.dual_node_detection) get_score() (in module pynibs.optimization.multichannel) get_score_raw() (in module pynibs.optimization.multichannel) get_score_raw_single_channel() (in module pynibs.optimization.multichannel) get_single_marker_file() (in module pynibs.expio.localite) get_smoothed_normals() (pynibs.roi.roi_structs.CorticalLayer method) get_sphere() (in module pynibs.mesh.utils) get_sphere_in_nii() (in module pynibs.roi.roi_utils) get_time_date() (in module pynibs.expio.Mep) get_tms_elements() (in module pynibs.expio.localite) get_trial_data_from_csv() (in module pynibs.expio.exp) get_virtual_mep_tvs() (in module pynibs.expio.Mep) gm_surf_fname (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) goal() (in module pynibs.optimization.multichannel) GRID_POINTS_PER_MM (pynibs.roi.roi_structs.CorticalLayer.Settings attribute)

H

hdf5_from_xml() (in module pynibs.expio.localite) hdf_2_ascii() (in module pynibs.hdf5_io.hdf5_io) head_circumference() (in module pynibs.mesh.utils) header_data (pynibs.expio.brainsight.BrainsightCSVParser attribute)

header_file (pynibs.expio.brainsight.BrainsightCSVParser attribute) hermite_rodriguez_1st() (in module pynibs.muap) hotspots_by_score_cumulative() (in module pynibs.regression.dual_node_detection) hotspots_by_score_percentiles() (in module pynibs.regression.dual_node_detection)

I

id (pynibs.subject.Subject.self attribute) identify_network_type() (in module pynibs.regression.dual_node_detection) identify_shape() (in module pynibs.regression.dual_node_detection) in_hull() (in module pynibs.mesh.utils) init() (in module pynibs.regression.regression)

init_fim_matrix() (in module pynibs.optimization.opt_mep) init_from_file() (pynibs.roi.roi_structs.CorticalLayer class method) init_from_surface() (pynibs.roi.roi_structs.CorticalLayer class method) intensity_thresh() (in module pynibs.congruence.stimulation_threshold) intersection_vec_plan() (in module pynibs.util.utils) invert() (in module pynibs.util.utils)

L

layer (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) likelihood_posterior() (in module pynibs.util.utils) linear() (in module pynibs.expio.fit_funs) linear_log() (in module pynibs.expio.fit_funs) list2dict() (in module pynibs.util.utils) load_cell_model() (in module pynibs.neuron.neuron_regression) load_matsimnibs_txt() (in module pynibs.expio.exp)

load_mesh_hdf5() (in module pynibs.hdf5_io.hdf5_io) load_mesh_msh() (in module pynibs.hdf5_io.hdf5_io) load_muaps() (in module pynibs.util.utils) load_roi_surface_obj_from_hdf5() (in module pynibs.roi.roi_utils) load_subject() (in module pynibs.subject) load_subject_hdf5() (in module pynibs.subject) load_subject_pkl() (in module pynibs.subject) logistic_regression() (in module pynibs.regression.regression)

M

make_average_subject() (in module pynibs.freesurfer) make_GM_WM_surface() (in module pynibs.roi.roi_utils) (pynibs.roi.roi_structs.RegionOfInterestSurface method) make_group_average() (in module pynibs.freesurfer) make_roi_volume_from_msh() (pynibs.roi.roi_structs.RegionOfInterestVolume method) map_data_to_surface() (in module pynibs.mesh.transformations) map_nii2surf() (in module pynibs.mesh.transformations) marker_is_empty() (in module pynibs.expio.localite) markers_are_empty() (in module pynibs.expio.localite) match_behave_and_triggermarker() (in module pynibs.expio.localite) match_instrument_marker_file() (in module pynibs.expio.localite) match_instrument_marker_string() (in module pynibs.expio.localite) match_tm_to_im() (in module pynibs.expio.localite) matsim2paraview() (in module pynibs.util.rotations) maximality_focality_optimization() (in module pynibs.optimization.multichannel) mc() (in module pynibs.optimization.workhorses) mean_mep_threshold() (in module pynibs.congruence.stimulation_threshold) median_sampled_pairwise_sqdist() (in module pynibs.optimization.coil_sampling) Mep (class in pynibs.expio.Mep) merge_exp_data_brainsight() (in module pynibs.expio.brainsight) merge_exp_data_cobot() (in module pynibs.expio.cobot) merge_exp_data_ft() (in module pynibs.expio.localite) merge_exp_data_localite() (in module pynibs.expio.localite) merge_exp_data_rt() (in module pynibs.expio.localite) merge_exp_data_visor() (in module pynibs.expio.visor) Mesh (class in pynibs.mesh.mesh_struct) midlayer_2_surf() (in module pynibs.mesh.transformations) module pynibs pynibs.coil pynibs.coil.coil pynibs.coil.export pynibs.congruence pynibs.congruence.congruence pynibs.congruence.ext_metrics pynibs.congruence.stimulation_threshold pynibs.expio pynibs.expio.brainsight pynibs.expio.brainvis pynibs.expio.cobot pynibs.expio.exp pynibs.expio.fit_funs pynibs.expio.invesalius pynibs.expio.localite pynibs.expio.Mep pynibs.expio.neurone pynibs.expio.signal_ced pynibs.expio.visor pynibs.freesurfer pynibs.hdf5_io pynibs.hdf5_io.hdf5_io pynibs.hdf5_io.xdmf pynibs.mesh pynibs.mesh.mesh_struct pynibs.mesh.transformations pynibs.mesh.utils pynibs.models pynibs.muap pynibs.neuron pynibs.neuron.neuron_regression pynibs.neuron.util pynibs.optimization pynibs.optimization.coil_opt pynibs.optimization.coil_sampling pynibs.optimization.multichannel pynibs.optimization.opt_mep pynibs.optimization.workhorses pynibs.pckg pynibs.pckg.libeep pynibs.regression pynibs.regression.dual_node_detection pynibs.regression.regression pynibs.roi pynibs.roi.roi_structs pynibs.roi.roi_utils pynibs.subject pynibs.tensor_scaling pynibs.tms_pulse pynibs.util pynibs.util.dosing pynibs.util.quality_measures pynibs.util.rotations pynibs.util.utils pynibs.visualization pynibs.visualization.plot_2D pynibs.visualization.render_3D

msh2hdf5() (in module pynibs.hdf5_io.hdf5_io) mt (pynibs.expio.Mep.Mep attribute) mutual_coherence() (in module pynibs.util.utils)

N

N_points (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) N_region (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) N_tet (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) N_tri (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) network_detection_algorithm_application() (in module pynibs.regression.dual_node_detection) network_detection_algorithm_testing() (in module pynibs.regression.dual_node_detection) nii2msh() (in module pynibs.roi.roi_utils) nl_hdf5() (in module pynibs.regression.regression) nl_hdf5_single_core() (in module pynibs.regression.regression) nl_hdf5_single_core_write() (in module pynibs.regression.regression)

nnav2simnibs() (in module pynibs.expio.exp) node_coord (pynibs.roi.roi_structs.RegionOfInterestVolume attribute) node_coord_low (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) node_coord_mid (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) node_coord_up (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) node_number_list (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) norm_percentile() (in module pynibs.util.utils) normalize_rot() (in module pynibs.util.rotations) nrmsd() (in module pynibs.util.quality_measures) nrmse() (in module pynibs.util.quality_measures) NUM_TRIANGLE_SMOOTHING_STEPS (pynibs.roi.roi_structs.CorticalLayer.Settings attribute)

O

online_optimization() (in module pynibs.optimization.coil_opt) opt_coil_placement_order() (in module pynibs.coil.coil) optimal_coilplacement_region() (in module pynibs.optimization.coil_opt) optimization_all_k() (in module pynibs.optimization.multichannel)

optimization_roi() (in module pynibs.optimization.multichannel) optimize_currents() (in module pynibs.optimization.multichannel) optimize_currents_single_channel() (in module pynibs.optimization.multichannel) outliers_mask() (in module pynibs.expio.exp) overstimulated_area() (in module pynibs.optimization.multichannel)

P

parse_line() (pynibs.expio.brainsight.BrainsightCSVParser method), [1] plot() (pynibs.expio.Mep.Mep method) plot_data_bin() (in module pynibs.regression.dual_node_detection) plot_data_clf() (in module pynibs.regression.dual_node_detection) plot_data_std() (in module pynibs.regression.dual_node_detection) plot_io_curve() (in module pynibs.visualization.plot_2D) plot_tms_motion_parameter() (in module pynibs.util.quality_measures) point_data_to_cell_data_vtk() (in module pynibs.mesh.transformations) points_to_triangles() (in module pynibs.util.rotations) popt (pynibs.expio.Mep.Mep attribute) popt_sig (pynibs.expio.Mep.Mep attribute) print() (pynibs.mesh.mesh_struct.Mesh method) (pynibs.mesh.mesh_struct.ROI method) print_attrs() (in module pynibs.hdf5_io.hdf5_io) print_time() (in module pynibs.expio.exp) project_on_midlayer() (pynibs.roi.roi_structs.RegionOfInterestSurface method) project_on_scalp() (in module pynibs.mesh.transformations) project_on_scalp_hdf5() (in module pynibs.mesh.transformations) pstd (pynibs.expio.Mep.Mep attribute) pynibs module pynibs.coil module pynibs.coil.coil module pynibs.coil.export module pynibs.congruence module pynibs.congruence.congruence module pynibs.congruence.ext_metrics module pynibs.congruence.stimulation_threshold module pynibs.expio module pynibs.expio.brainsight module pynibs.expio.brainvis module pynibs.expio.cobot module pynibs.expio.exp module pynibs.expio.fit_funs module pynibs.expio.invesalius module pynibs.expio.localite module pynibs.expio.Mep module pynibs.expio.neurone module pynibs.expio.signal_ced module pynibs.expio.visor module pynibs.freesurfer module pynibs.hdf5_io module pynibs.hdf5_io.hdf5_io module pynibs.hdf5_io.xdmf module

pynibs.mesh module pynibs.mesh.mesh_struct module pynibs.mesh.transformations module pynibs.mesh.utils module pynibs.models module pynibs.muap module pynibs.neuron module pynibs.neuron.neuron_regression module pynibs.neuron.util module pynibs.optimization module pynibs.optimization.coil_opt module pynibs.optimization.coil_sampling module pynibs.optimization.multichannel module pynibs.optimization.opt_mep module pynibs.optimization.workhorses module pynibs.pckg module pynibs.pckg.libeep module pynibs.regression module pynibs.regression.dual_node_detection module pynibs.regression.regression module pynibs.roi module pynibs.roi.roi_structs module pynibs.roi.roi_utils module pynibs.subject module pynibs.tensor_scaling module pynibs.tms_pulse module pynibs.util module pynibs.util.dosing module pynibs.util.quality_measures module pynibs.util.rotations module pynibs.util.utils module pynibs.visualization module pynibs.visualization.plot_2D module pynibs.visualization.render_3D module

Q

quat_rotation_angle() (in module pynibs.util.rotations) quat_to_rot() (in module pynibs.util.rotations)

quaternion_conjugate() (in module pynibs.util.rotations) quaternion_diff() (in module pynibs.util.rotations) quaternion_inverse() (in module pynibs.util.rotations)

R

radius (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) random_walk_coil() (in module pynibs.coil.coil) rd() (in module pynibs.util.utils) read_arr_from_hdf5() (in module pynibs.hdf5_io.hdf5_io) read_biosig_emg_data() (in module pynibs.expio.signal_ced) read_channel_names() (in module pynibs.expio.brainvis) read_coil() (in module pynibs.expio.localite) read_csv() (in module pynibs.expio.exp) read_curv_data() (in module pynibs.freesurfer) read_data_hdf5() (in module pynibs.hdf5_io.hdf5_io) read_dict_from_hdf5() (in module pynibs.hdf5_io.hdf5_io) read_exp_stimulations() (in module pynibs.expio.exp) read_nlr() (in module pynibs.expio.visor) read_roi_from_geo_fn() (in module pynibs.roi.roi_utils) read_roi_from_mesh_hdf5() (in module pynibs.roi.roi_utils) read_samples_brainsight() (in module pynibs.expio.brainsight) read_sampling_frequency() (in module pynibs.expio.brainvis) read_targets_brainsight() (in module pynibs.expio.brainsight) read_triggermarker() (in module pynibs.expio.brainsight) (in module pynibs.expio.invesalius) (in module pynibs.expio.localite) read_triggermarker_localite() (in module pynibs.expio.localite) recursive_len() (in module pynibs.util.utils) refine_surface() (in module pynibs.mesh.transformations)

region (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) RegionOfInterestSurface (class in pynibs.roi.roi_structs) RegionOfInterestVolume (class in pynibs.roi.roi_structs) regress_data() (in module pynibs.regression.regression) remove_unconnected_surfaces() (pynibs.roi.roi_structs.CorticalLayer method) render_coil_positions() (in module pynibs.visualization.render_3D) render_data_on_surface() (in module pynibs.visualization.render_3D) rescale_lambda_centerized() (in module pynibs.tensor_scaling) rescale_lambda_centerized_workhorse() (in module pynibs.tensor_scaling) ridge_from_hdf5() (in module pynibs.regression.regression) ROI (class in pynibs.mesh.mesh_struct) roi_bbox_from_points() (pynibs.roi.roi_structs.CorticalLayer static method) roi_elmt_wise_corr() (in module pynibs.optimization.workhorses) ROI_SIZE_OFFSET (pynibs.roi.roi_structs.CorticalLayer.Settings attribute) rot_to_quat() (in module pynibs.util.rotations) rotate_matsimnibs_euler() (in module pynibs.util.rotations) rotation_matrix_to_euler_angles() (in module pynibs.util.rotations) rotmat_from_vecs() (in module pynibs.util.rotations) rowvec_diff() (in module pynibs.optimization.coil_opt) (in module pynibs.optimization.workhorses) rowvec_diff_prepare() (in module pynibs.optimization.workhorses) rsd_inverse_workhorse() (in module pynibs.congruence.ext_metrics) run_fit() (pynibs.regression.regression.Element method) run_fit_multistart() (pynibs.expio.Mep.Mep method) run_select_signed_data() (pynibs.regression.regression.Element method)

S

sample_sphere() (in module pynibs.mesh.utils) save() (pynibs.roi.roi_structs.CorticalLayer method) save_matsimnibs_txt() (in module pynibs.expio.exp) save_subject() (in module pynibs.subject) save_subject_hdf5() (in module pynibs.subject) save_subject_pkl() (in module pynibs.subject) scale_e_for_dvs() (in module pynibs.expio.Mep) scd() (in module pynibs.optimization.multichannel) set_constants() (pynibs.regression.regression.Element method) set_init_vals() (pynibs.regression.regression.Element method) set_limits() (pynibs.regression.regression.Element method) set_random_init_vals() (pynibs.regression.regression.Element method) setup_model() (pynibs.regression.regression.Element method) sfap() (in module pynibs.muap) sfap_dip() (in module pynibs.muap) shift_coil_to_skin() (in module pynibs.coil.coil) shift_many_coil_placements() (in module pynibs.coil.coil) sigmoid() (in module pynibs.expio.fit_funs) sigmoid4() (in module pynibs.expio.fit_funs) sigmoid4_log() (in module pynibs.expio.fit_funs) sigmoid_log() (in module pynibs.expio.fit_funs) sigmoid_log_p() (in module pynibs.util.utils) sigmoid_thresh() (in module pynibs.congruence.stimulation_threshold)

simnibs2brainsight() (in module pynibs.expio.brainsight) simnibs_results_msh2hdf5() (in module pynibs.hdf5_io.hdf5_io) simnibs_results_msh2hdf5_workhorse() (in module pynibs.hdf5_io.hdf5_io) sing_elm_fitted() (in module pynibs.regression.regression) sing_elm_raw() (in module pynibs.regression.regression) single_fit() (in module pynibs.regression.regression) SKIPPING (pynibs.expio.brainsight.BrainsightCSVParser.State attribute) smooth() (in module pynibs.optimization.workhorses) sort_by_condition() (in module pynibs.expio.exp) sort_data_by_condition() (in module pynibs.expio.exp) sort_opt_coil_positions() (in module pynibs.coil.coil) sphere() (in module pynibs.optimization.multichannel) split_hdf5() (in module pynibs.hdf5_io.hdf5_io) splitext_niigz() (in module pynibs.expio.exp) square() (in module pynibs.expio.exp) step() (in module pynibs.expio.fit_funs) stepdown_approach() (in module pynibs.regression.regression) stimulation_threshold() (in module pynibs.congruence.stimulation_threshold) strain_constr() (in module pynibs.optimization.multichannel) strain_constr_min() (in module pynibs.optimization.multichannel) Subject (class in pynibs.subject) subsample() (pynibs.roi.roi_structs.RegionOfInterestSurface method) svd() (in module pynibs.optimization.workhorses)

T

TAG_GRAY_MATTER_SURF (pynibs.roi.roi_structs.CorticalLayer.Settings attribute) TAG_GRAY_MATTER_VOL (pynibs.roi.roi_structs.CorticalLayer.Settings attribute) TAG_WHITE_MATTER_SURF (pynibs.roi.roi_structs.CorticalLayer.Settings attribute) TAG_WHITE_MATTER_VOL (pynibs.roi.roi_structs.CorticalLayer.Settings attribute) tal2mni() (in module pynibs.util.utils) target_to_max_ratio() (in module pynibs.optimization.multichannel) template (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) test_coil_position_gpc() (in module pynibs.coil.coil) tet_idx_node_coord (pynibs.roi.roi_structs.RegionOfInterestVolume attribute) tet_idx_node_coord_mid (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) tet_idx_tetrahedra_center (pynibs.roi.roi_structs.RegionOfInterestVolume attribute) tet_idx_tri_center_low (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) tet_idx_tri_center_mid (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) tet_idx_tri_center_up (pynibs.roi.roi_structs.RegionOfInterestSurface attribute)

tet_idx_triangle_center (pynibs.roi.roi_structs.RegionOfInterestVolume attribute) tet_node_number_list (pynibs.roi.roi_structs.RegionOfInterestVolume attribute) tetrahedra_center (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) tetrahedra_volume (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) TetrahedraLinear (class in pynibs.mesh.mesh_struct) tets_in_sphere() (in module pynibs.mesh.utils) toRAS() (in module pynibs.expio.exp) transform_brainsight() (in module pynibs.expio.brainsight) tri_center_coord_low (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) tri_center_coord_mid (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) tri_center_coord_up (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) tri_node_number_list (pynibs.roi.roi_structs.RegionOfInterestVolume attribute) triangles_center (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) triangles_normal (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) tris_in_sphere() (in module pynibs.mesh.utils)

U

unique_rows() (in module pynibs.util.utils)

V

var() (in module pynibs.optimization.workhorses)

variability() (in module pynibs.optimization.workhorses)

W

weight_signal_matrix() (in module pynibs.muap) whole_network_detection() (in module pynibs.regression.dual_node_detection) wm_surf_fname (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) workhorse_element_init() (in module pynibs.regression.regression) workhorse_element_run_fit() (in module pynibs.regression.regression) workhorse_interp() (in module pynibs.neuron.neuron_regression) write_arr_to_hdf5() (in module pynibs.hdf5_io.hdf5_io) write_coil_hdf5() (in module pynibs.hdf5_io.hdf5_io) write_coil_pos_hdf5() (in module pynibs.coil.export) write_coil_sequence_xdmf() (in module pynibs.hdf5_io.xdmf) write_csv() (in module pynibs.expio.exp) write_data_hdf5() (in module pynibs.hdf5_io.hdf5_io) write_data_hdf5_surf() (in module pynibs.hdf5_io.hdf5_io) write_data_hdf5_vol() (in module pynibs.hdf5_io.hdf5_io) write_dict_to_hdf5() (in module pynibs.hdf5_io.hdf5_io) write_effect_map_hdf5() (in module pynibs.regression.dual_node_detection) write_geo_hdf5() (in module pynibs.hdf5_io.hdf5_io)

write_geo_hdf5_surf() (in module pynibs.hdf5_io.hdf5_io) write_geo_hdf5_vol() (in module pynibs.hdf5_io.hdf5_io) write_hotspot_scoremap_hdf5() (in module pynibs.regression.dual_node_detection) write_magventure_xls() (in module pynibs.optimization.multichannel) write_nda_application_results_csv() (in module pynibs.regression.dual_node_detection) write_nda_test_results_csv() (in module pynibs.regression.dual_node_detection) write_network_detection_data_hdf5() (in module pynibs.regression.dual_node_detection) write_regression_hdf5() (in module pynibs.regression.regression) write_targets_brainsight() (in module pynibs.expio.brainsight) write_temporal_xdmf() (in module pynibs.hdf5_io.xdmf) write_to_hdf5() (pynibs.mesh.mesh_struct.Mesh method) (pynibs.mesh.mesh_struct.ROI method) write_triggermarker_stats() (in module pynibs.expio.exp) write_vtu() (in module pynibs.mesh.transformations) write_xdmf() (in module pynibs.hdf5_io.xdmf) write_xdmf_coordinates() (in module pynibs.hdf5_io.xdmf) write_xdmf_surf() (in module pynibs.hdf5_io.xdmf)

X

x_limits (pynibs.expio.Mep.Mep attribute)

X_ROI (pynibs.roi.roi_structs.RegionOfInterestSurface attribute)

Y

y_limits (pynibs.expio.Mep.Mep attribute)

Y_ROI (pynibs.roi.roi_structs.RegionOfInterestSurface attribute)

Z

Z_ROI (pynibs.roi.roi_structs.RegionOfInterestSurface attribute)