Index

A

add_center() (in module pynibs.util.util) add_channel() (in module pynibs.pckg.libeep.pyeep) 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_samples() (in module pynibs.pckg.libeep.pyeep) add_sigmoidal_bestfit() (in module pynibs.expio.exp) arrays_similar() (in module pynibs.expio.localite)

B

bases2rotmat() (in module pynibs.util.rotations) bash() (in module pynibs.util.util) bash_call() (in module pynibs.util.util)

BrainsightCSVParser (class in pynibs.expio.brainsight) BrainsightCSVParser.State (class in pynibs.expio.brainsight) 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) calc_coil_transformation_matrix() (in module pynibs.coil) calc_E() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_e_effective() (in module pynibs.neuron.neuron_regression) calc_e_in_midlayer_roi() (in module pynibs.util.simnibs) 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_gradient() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_J() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_motor_threshold() (pynibs.expio.Mep.Mep method) calc_n_network_combs() (in module pynibs.util.util) calc_opt_gain_map() (in module pynibs.optimization.optimization) 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_QOI_in_points() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_QOI_in_points_tet_idx() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_surface_adjacent_tetrahedra_idx_list() (pynibs.mesh.mesh_struct.TetrahedraLinear method) calc_tms_motion_params() (in module pynibs.util.quality_measures) center (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) cfs2hdf5() (in module pynibs.expio.signal_ced) check_coil_position() (in module pynibs.coil) check_file_and_format() (in module pynibs.subject) check_mesh() (in module pynibs.util.simnibs) check_state_transition() (pynibs.expio.brainsight.BrainsightCSVParser method), [1] clean_roi() (in module pynibs.roi.roi) close() (in module pynibs.pckg.libeep.pyeep) close_channel_info() (in module pynibs.pckg.libeep.pyeep)

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.util) compute_pcd() (in module pynibs.util.quality_measures) convert_csv_to_hdf5() (in module pynibs.expio.exp) copt (pynibs.expio.Mep.Mep attribute) 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_channel_info() (in module pynibs.pckg.libeep.pyeep) 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_plot_settings_dict() (in module pynibs.subject) create_position_path_xdmf() (in module pynibs.hdf5_io.xdmf) create_refine_spherical_roi() (in module pynibs.roi.roi) create_stimsite_from_exp_hdf5() (in module pynibs.coil) create_stimsite_from_list() (in module pynibs.coil) create_stimsite_from_matsimnibs() (in module pynibs.coil) create_stimsite_from_tmslist() (in module pynibs.coil) create_stimsite_hdf5() (in module pynibs.coil) 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.util) cross_product_einsum2() (in module pynibs.util.util) current_state (pynibs.expio.brainsight.BrainsightCSVParser attribute)

D

data (pynibs.expio.brainsight.BrainsightCSVParser attribute) DATA (pynibs.expio.brainsight.BrainsightCSVParser.State attribute) data_elements2nodes() (pynibs.mesh.mesh_struct.TetrahedraLinear method) DATA_HEADER (pynibs.expio.brainsight.BrainsightCSVParser.State attribute) data_nodes2elements() (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_element_idx_in_mesh() (in module pynibs.roi.roi) (pynibs.roi.roi_structs.RegionOfInterestSurface method) DI_wave() (in module pynibs.neuron.util) differential_evolution() (in module pynibs.util.util) dist() (in module pynibs.optimization.workhorses) dist_mc() (in module pynibs.optimization.workhorses) dist_svd() (in module pynibs.optimization.workhorses) dummy_fun() (in module pynibs.expio.fit_funs)

E

e_field_angle_theta() (in module pynibs.util.simnibs) e_field_gradient_between_wm_gm() (in module pynibs.util.simnibs) elem_workhorse() (in module pynibs.roi.roi) 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) 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)

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) fit (pynibs.expio.Mep.Mep attribute)

fit_mep_to_function() (pynibs.expio.Mep.Mep method) fit_mep_to_function_multistart() (pynibs.expio.Mep.Mep method) fix_mesh() (in module pynibs.util.simnibs) 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) 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.util) 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_cartesian_product() (in module pynibs.util.util) get_channel_count() (in module pynibs.pckg.libeep.pyeep) get_channel_label() (in module pynibs.pckg.libeep.pyeep) get_channel_reference() (in module pynibs.pckg.libeep.pyeep) get_channel_unit() (in module pynibs.pckg.libeep.pyeep) get_cnt_data() (in module pynibs.expio.visor) get_cnt_infos() (in module pynibs.expio.exp) get_coil_dipole_pos() (in module pynibs.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_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_ft_data_from_csv() (in module pynibs.expio.exp) get_instrument_marker() (in module pynibs.expio.visor) get_invalid_coil_parameters() (in module pynibs.coil) get_marker() (in module pynibs.expio.brainsight) (in module pynibs.expio.localite) get_mask() (in module pynibs.roi.roi) get_mep_elements() (in module pynibs.expio.Mep)

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_opt_mat() (in module pynibs.util.simnibs) get_optimal_coil_positions() (in module pynibs.optimization.optimization) 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_sample_count() (in module pynibs.pckg.libeep.pyeep) get_sample_frequency() (in module pynibs.pckg.libeep.pyeep) get_samples() (in module pynibs.pckg.libeep.pyeep) 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_skin_cortex_distance() (in module pynibs.util.simnibs) get_smoothed_normals() (pynibs.roi.roi_structs.CorticalLayer method) get_sphere_in_nii() (in module pynibs.roi.roi) 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_trigger() (in module pynibs.pckg.libeep.pyeep) get_trigger_count() (in module pynibs.pckg.libeep.pyeep) get_version() (in module pynibs.pckg.libeep.pyeep) get_virtual_mep_tvs() (in module pynibs.expio.Mep) gm_surf_fname (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) GRID_POINTS_PER_MM (pynibs.roi.roi_structs.CorticalLayer.Settings attribute)

H

hdf_2_ascii() (in module pynibs.hdf5_io.hdf5_io)

header_data (pynibs.expio.brainsight.BrainsightCSVParser attribute) header_file (pynibs.expio.brainsight.BrainsightCSVParser attribute)

I

id (pynibs.subject.Subject.self attribute) 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) intersection_vec_plan() (in module pynibs.util.util) invert() (in module pynibs.util.util)

L

layer (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) likelihood_posterior() (in module pynibs.util.util) linear() (in module pynibs.expio.fit_funs) linear_log() (in module pynibs.expio.fit_funs) list2dict() (in module pynibs.util.util) 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.util) load_roi_surface_obj_from_hdf5() (in module pynibs.roi.roi) load_subject() (in module pynibs.subject) load_subject_hdf5() (in module pynibs.subject) load_subject_pkl() (in module pynibs.subject)

M

make_average_subject() (in module pynibs.freesurfer) make_GM_WM_surface() (in module pynibs.roi.roi) (pynibs.roi.roi_structs.RegionOfInterestSurface method) make_group_average() (in module pynibs.freesurfer) make_roi_volume_from_msh() (pynibs.roi.roi_structs.RegionOfInterestVolume method) 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) mc() (in module pynibs.optimization.workhorses) Mep (class in pynibs.expio.Mep) merge_exp_data_brainsight() (in module pynibs.expio.brainsight) 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) module pynibs.coil pynibs.expio pynibs.expio.brainsight pynibs.expio.brainvis pynibs.expio.exp pynibs.expio.fit_funs pynibs.expio.localite pynibs.expio.Mep pynibs.expio.signal_ced pynibs.expio.visor pynibs.freesurfer pynibs.hdf5_io pynibs.hdf5_io.hdf5_io pynibs.hdf5_io.xdmf pynibs.mesh.mesh_struct pynibs.models pynibs.neuron pynibs.neuron.neuron_regression pynibs.neuron.util pynibs.optimization pynibs.optimization.multichannel pynibs.optimization.opt_mep pynibs.optimization.optimization pynibs.optimization.workhorses pynibs.pckg pynibs.pckg.libeep pynibs.pckg.libeep.pyeep pynibs.roi pynibs.roi.roi pynibs.roi.roi_structs pynibs.subject pynibs.tensor_scaling pynibs.util pynibs.util.quality_measures pynibs.util.rotations pynibs.util.simnibs pynibs.util.util

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

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) nii2msh() (in module pynibs.roi.roi) 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.util) 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.optimization) optimal_coilplacement_region() (in module pynibs.optimization.optimization)

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

P

parse_line() (pynibs.expio.brainsight.BrainsightCSVParser method), [1] plot() (pynibs.expio.Mep.Mep method) plot_tms_motion_parameter() (in module pynibs.util.quality_measures) popt (pynibs.expio.Mep.Mep attribute) popt_sig (pynibs.expio.Mep.Mep attribute) precompute_geo_info_for_layer_field_interpolation() (in module pynibs.util.simnibs) 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) pstd (pynibs.expio.Mep.Mep attribute) pynibs.coil module pynibs.expio module pynibs.expio.brainsight module pynibs.expio.brainvis module pynibs.expio.exp module pynibs.expio.fit_funs module pynibs.expio.localite module pynibs.expio.Mep 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.mesh_struct module pynibs.models module

pynibs.neuron module pynibs.neuron.neuron_regression module pynibs.neuron.util module pynibs.optimization module pynibs.optimization.multichannel module pynibs.optimization.opt_mep module pynibs.optimization.optimization module pynibs.optimization.workhorses module pynibs.pckg module pynibs.pckg.libeep module pynibs.pckg.libeep.pyeep module pynibs.roi module pynibs.roi.roi module pynibs.roi.roi_structs module pynibs.subject module pynibs.tensor_scaling module pynibs.util module pynibs.util.quality_measures module pynibs.util.rotations module pynibs.util.simnibs module pynibs.util.util 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) rd() (in module pynibs.util.util) read() (in module pynibs.pckg.libeep.pyeep) read_arr_from_hdf5() (in module pynibs.hdf5_io.hdf5_io) read_biosig_emg_data() (in module pynibs.expio.Mep) read_channel_names() (in module pynibs.expio.brainvis) read_coil() (in module pynibs.expio.localite) read_coil_geo() (in module pynibs.util.simnibs) 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_mesh_hdf5() (in module pynibs.roi.roi) 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.localite)

read_triggermarker_localite() (in module pynibs.expio.localite) recursive_len() (in module pynibs.util.util) region (pynibs.mesh.mesh_struct.TetrahedraLinear attribute) RegionOfInterestSurface (class in pynibs.roi.roi_structs) RegionOfInterestVolume (class in pynibs.roi.roi_structs) remove_unconnected_surfaces() (pynibs.roi.roi_structs.CorticalLayer method) rescale_lambda_centerized() (in module pynibs.tensor_scaling) rescale_lambda_centerized_workhorse() (in module pynibs.tensor_scaling) 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.optimization) (in module pynibs.optimization.workhorses) rowvec_diff_prepare() (in module pynibs.optimization.workhorses) run_fit_multistart() (pynibs.expio.Mep.Mep method)

S

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) 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.util) 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) SKIPPING (pynibs.expio.brainsight.BrainsightCSVParser.State attribute) smooth() (in module pynibs.optimization.workhorses) smooth_mesh() (in module pynibs.util.simnibs) 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) split_hdf5() (in module pynibs.hdf5_io.hdf5_io) splitext_niigz() (in module pynibs.expio.exp) square() (in module pynibs.expio.exp) 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.util) template (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) test_coil_position_gpc() (in module pynibs.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) 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)

U

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

V

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

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

W

wm_surf_fname (pynibs.roi.roi_structs.RegionOfInterestSurface attribute) workhorse_interp() (in module pynibs.neuron.neuron_regression) write_arr_to_hdf5() (in module pynibs.hdf5_io.hdf5_io) write_cnt() (in module pynibs.pckg.libeep.pyeep) write_coil_hdf5() (in module pynibs.hdf5_io.hdf5_io) write_coil_pos_hdf5() (in module pynibs.coil) 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_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_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_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)