Index

A

as_directory() (in module pynets.core.utils) as_list() (in module pynets.core.utils) autofix() (in module pynets.core.thresholding)

average_local_efficiency() (in module pynets.statistics.individual.algorithms) average_shortest_path_length_fast() (in module pynets.statistics.individual.algorithms) average_shortest_path_length_for_all() (in module pynets.statistics.individual.algorithms)

B

binarize() (in module pynets.core.thresholding) build_args_from_config() (in module pynets.core.utils) build_asetomes() (in module pynets.statistics.individual.spectral)

build_masetome() (in module pynets.statistics.individual.spectral) build_multigraphs() (in module pynets.statistics.individual.multiplex) build_mx_multigraph() (in module pynets.statistics.individual.multiplex) build_omnetome() (in module pynets.statistics.individual.spectral)

C

check_est_path_existence() (in module pynets.core.utils) check_template_loads() (in module pynets.core.utils) checkConsecutive() (in module pynets.core.utils) collect_pandas_df() (in module pynets.core.utils) collect_pandas_df_make() (in module pynets.statistics.individual.algorithms) collectpandasjoin() (in module pynets.core.utils) community_resolution_selection() (in module pynets.statistics.individual.algorithms) coords_masker() (in module pynets.core.nodemaker) countmotifs() (in module pynets.statistics.individual.algorithms) create_anisopowermap() (in module pynets.dmri.estimation) create_communities() (in module pynets.statistics.individual.algorithms)

create_csv_path() (in module pynets.core.utils) create_density_map() (in module pynets.dmri.track) create_est_path_diff() (in module pynets.core.utils) create_est_path_func() (in module pynets.core.utils) create_gb_palette() (in module pynets.plotting.brain) create_parcel_atlas() (in module pynets.core.nodemaker) create_raw_path_diff() (in module pynets.core.utils) create_raw_path_func() (in module pynets.core.utils) create_spherical_roi_volumes() (in module pynets.core.nodemaker) csa_mod_est() (in module pynets.dmri.estimation) csd_mod_est() (in module pynets.dmri.estimation)

D

decompress_nifti() (in module pynets.core.utils) defragment() (in module pynets.statistics.individual.algorithms) density_thresholding() (in module pynets.core.thresholding) discretisation() (in module pynets.fmri.clustering) disparity_filter() (in module pynets.core.thresholding) disparity_filter_alpha_cut() (in module pynets.core.thresholding)

diversity_coef_sign() (in module pynets.statistics.individual.algorithms) dmri_connectometry() (in module pynets.core.workflows) do_dir_path() (in module pynets.core.utils) drop_badixs_from_parcellation() (in module pynets.core.nodemaker) drop_coords_labels_from_restricted_parcellation() (in module pynets.core.nodemaker) dumpstacks() (in module pynets.core.utils)

E

enforce_hem_distinct_consecutive_labels() (in module pynets.core.nodemaker) ensemble_parcellate() (in module pynets.fmri.clustering)

est_density() (in module pynets.core.thresholding) evaluate_streamline_plausibility() (in module pynets.dmri.utils) extract_b0() (in module pynets.dmri.utils)

F

fetch_nilearn_atlas_coords() (in module pynets.core.nodemaker) fill_confound_nans() (in module pynets.fmri.estimation)

filter_cols_from_targets() (in module pynets.core.utils) flatten() (in module pynets.core.utils) fmri_connectometry() (in module pynets.core.workflows)

G

gen_network_parcels() (in module pynets.core.nodemaker) generate_seeds() (in module pynets.dmri.utils) generate_sl() (in module pynets.dmri.utils) get_betweenness_centrality() (in module pynets.statistics.individual.algorithms) get_clustering() (in module pynets.statistics.individual.algorithms) get_comm_centrality() (in module pynets.statistics.individual.algorithms) get_community() (in module pynets.statistics.individual.algorithms) get_conn_matrix() (in module pynets.fmri.estimation) get_degree_centrality() (in module pynets.statistics.individual.algorithms) get_diversity() (in module pynets.statistics.individual.algorithms) get_eigen_centrality() (in module pynets.statistics.individual.algorithms)

get_file() (in module pynets.core.utils) get_local_efficiency() (in module pynets.statistics.individual.algorithms) get_names_and_coords_of_parcels() (in module pynets.core.nodemaker) get_node_attributes() (in module pynets.core.nodemaker) get_node_membership() (in module pynets.core.nodemaker) get_optimal_cov_estimator() (in module pynets.fmri.estimation) get_participation() (in module pynets.statistics.individual.algorithms) get_prop_type() (in module pynets.statistics.individual.algorithms) get_rich_club_coeff() (in module pynets.statistics.individual.algorithms) get_sphere() (in module pynets.core.nodemaker) get_template_tf() (in module pynets.core.utils) global_efficiency() (in module pynets.statistics.individual.algorithms)

I

indx_1dto3d() (in module pynets.fmri.clustering) indx_3dto1d() (in module pynets.fmri.clustering)

invert() (in module pynets.core.thresholding) iterate_nx_global_measures() (in module pynets.statistics.individual.algorithms)

K

kill_process_family() (in module pynets.core.utils)

knn() (in module pynets.core.thresholding)

L

link_communities() (in module pynets.statistics.individual.algorithms) load_mat() (in module pynets.core.utils) load_mat_ext() (in module pynets.core.utils)

load_runconfig() (in module pynets.core.utils) local_efficiency() (in module pynets.statistics.individual.algorithms) local_thresholding_prop() (in module pynets.core.thresholding)

M

make_local_connectivity_scorr() (in module pynets.fmri.clustering) make_local_connectivity_tcorr() (in module pynets.fmri.clustering) mask_roi() (in module pynets.core.nodemaker) matching() (in module pynets.statistics.individual.multiplex) mcsd_mod_est() (in module pynets.dmri.estimation) merge_dicts() (in module pynets.core.utils) mergedicts() (in module pynets.core.utils) missing_elements() (in module pynets.core.utils) mmToVox() (in module pynets.core.nodemaker) module pynets pynets.core pynets.core.nodemaker pynets.core.thresholding pynets.core.utils pynets.core.workflows pynets.dmri pynets.dmri.estimation pynets.dmri.track pynets.dmri.utils pynets.fmri pynets.fmri.clustering pynets.fmri.estimation pynets.plotting pynets.plotting.adjacency pynets.plotting.brain pynets.statistics pynets.statistics.group pynets.statistics.group.benchmarking pynets.statistics.group.prediction pynets.statistics.individual pynets.statistics.individual.algorithms pynets.statistics.individual.multiplex pynets.statistics.individual.spectral pynets.statistics.utils

most_important() (in module pynets.statistics.individual.algorithms) mutual_information_2d() (in module pynets.statistics.individual.multiplex)

N

ncut() (in module pynets.fmri.clustering) nilearn_atlas_helper() (in module pynets.core.nodemaker) node_gen() (in module pynets.core.nodemaker) node_gen_masking() (in module pynets.core.nodemaker)

normalize() (in module pynets.core.thresholding) normalize_gradients() (in module pynets.dmri.utils) np2gt() (in module pynets.statistics.individual.algorithms) nx2gt() (in module pynets.statistics.individual.algorithms)

O

optimize_mutual_info() (in module pynets.statistics.individual.multiplex)

P

parcel_masker() (in module pynets.core.nodemaker) parcel_naming() (in module pynets.core.nodemaker) parcellate() (in module pynets.fmri.clustering) parcellate_ncut() (in module pynets.fmri.clustering) participation_coef() (in module pynets.statistics.individual.algorithms) participation_coef_sign() (in module pynets.statistics.individual.algorithms) pass_meta_ins() (in module pynets.core.utils) pass_meta_ins_multi() (in module pynets.core.utils) pass_meta_outs() (in module pynets.core.utils) perform_thresholding() (in module pynets.core.thresholding) plot_all_func() (in module pynets.plotting.brain) plot_all_struct() (in module pynets.plotting.brain) plot_all_struct_func() (in module pynets.plotting.brain) plot_community_conn_mat() (in module pynets.plotting.adjacency) plot_conn_mat() (in module pynets.plotting.adjacency) plot_conn_mat_func() (in module pynets.plotting.adjacency) plot_conn_mat_struct() (in module pynets.plotting.adjacency) plot_graph_measure_hists() (in module pynets.plotting.brain) plot_network_clusters() (in module pynets.plotting.brain) plot_timeseries() (in module pynets.plotting.brain) prep_tissues() (in module pynets.dmri.track) proportional() (in module pynets.fmri.clustering) prune_small_components() (in module pynets.statistics.individual.algorithms) prune_suffices() (in module pynets.core.utils) pynets module pynets.core module pynets.core.nodemaker module pynets.core.thresholding module pynets.core.utils module pynets.core.workflows module pynets.dmri module

pynets.dmri.estimation module pynets.dmri.track module pynets.dmri.utils module pynets.fmri module pynets.fmri.clustering module pynets.fmri.estimation module pynets.plotting module pynets.plotting.adjacency module pynets.plotting.brain module pynets.statistics module pynets.statistics.group module pynets.statistics.group.benchmarking module pynets.statistics.group.prediction module pynets.statistics.individual module pynets.statistics.individual.algorithms module pynets.statistics.individual.multiplex module pynets.statistics.individual.spectral module pynets.statistics.utils module

R

random_seeds_from_mask() (in module pynets.dmri.utils) raw_graph_workflow() (in module pynets.core.workflows) raw_mets() (in module pynets.statistics.individual.algorithms)

reconstruction() (in module pynets.dmri.estimation) rich_club_coefficient() (in module pynets.statistics.individual.algorithms) run() (pynets.core.utils.watchdog method) run_tracking() (in module pynets.dmri.track)

S

save_3d_to_4d() (in module pynets.core.utils) save_4d_to_3d() (in module pynets.core.utils) save_coords_and_labels_to_json() (in module pynets.core.utils) save_mat() (in module pynets.core.utils) save_mat_thresholded() (in module pynets.core.utils) save_nifti_parcels_map() (in module pynets.core.utils)

save_ts_to_file() (in module pynets.core.utils) sfm_mod_est() (in module pynets.dmri.estimation) show_template_bundles() (in module pynets.plotting.brain) smallworldness() (in module pynets.statistics.individual.algorithms) standardize() (in module pynets.core.thresholding) streams2graph() (in module pynets.dmri.estimation) subgraph_number_of_cliques_for_all() (in module pynets.statistics.individual.algorithms)

T

tens_mod_est() (in module pynets.dmri.estimation) tens_mod_fa_est() (in module pynets.dmri.estimation) thr2prob() (in module pynets.core.thresholding) three_to_four_parcellation() (in module pynets.core.nodemaker) thresh_func() (in module pynets.core.thresholding) thresh_raw_graph() (in module pynets.core.thresholding)

thresh_struct() (in module pynets.core.thresholding) threshold_absolute() (in module pynets.core.thresholding) threshold_proportional() (in module pynets.core.thresholding) timeout() (in module pynets.core.utils) timeseries_bootstrap() (in module pynets.fmri.estimation) track_ensemble() (in module pynets.dmri.track)

V

view_tractogram() (in module pynets.plotting.brain)

VoxTomm() (in module pynets.core.nodemaker)

W

watchdog (class in pynets.core.utils) weight_conversion() (in module pynets.core.thresholding)

weight_to_distance() (in module pynets.core.thresholding) weighted_transitivity() (in module pynets.statistics.individual.algorithms) workflow_selector() (in module pynets.core.workflows)