Index

_

__add__() (AFQ.api.bundle_dict.BundleDict method) __bool__() (AFQ.recognition.utils.SlsBeingRecognized method) __call__() (AFQ.utils.docs.GIFScraper method) (AFQ.utils.docs.PNGScraper method) __delitem__() (AFQ.api.bundle_dict.BundleDict method) __getitem__() (AFQ.api.bundle_dict.BundleDict method) __iter__() (AFQ.api.bundle_dict.BundleDict method) __len__() (AFQ.api.bundle_dict.BundleDict method) (AFQ.recognition.utils.SlsBeingRecognized method) __print__() (AFQ.api.bundle_dict.BundleDict method) __repr__() (AFQ.utils.docs.GIFScraper method) (AFQ.utils.docs.PNGScraper method) __setitem__() (AFQ.api.bundle_dict.BundleDict method) _add_bundle_to_fiber_group() (in module AFQ.recognition.recognize) _add_bundle_to_meta() (in module AFQ.recognition.recognize) _color_arr2str() (in module AFQ.viz.plotly_backend) _compute_mean_euclidean_matrix() (in module AFQ.recognition.clustering) _cond_load() (AFQ.api.bundle_dict.BundleDict method) _cond_load_bundle() (AFQ.api.bundle_dict.BundleDict method) _dict (AFQ.api.bundle_dict.BundleDict attribute) _distance_to_similarity() (in module AFQ.recognition.clustering) _draw_core() (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend)

_draw_roi() (in module AFQ.viz.plotly_backend) _draw_slice() (in module AFQ.viz.plotly_backend) _draw_streamlines() (in module AFQ.viz.plotly_backend) _fiber_odf() (in module AFQ.tasks.tractography) _ga_id (in module AFQ) _inline_interact() (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend) _interp_arr_with_affine() (in module AFQ.recognition.roi) _is_int() (in module AFQ.tractography.utils) _meta_from_tracking_params() (in module AFQ.tasks.tractography) _name_from_enum() (in module AFQ.viz.plotly_backend) _or_to_text() (in module AFQ.tasks.data) _plot_profiles() (in module AFQ.viz.plotly_backend) _prepare_bundle_def() (in module AFQ.recognition.criteria) _rectangular_similarity_matrix() (in module AFQ.recognition.clustering) _return_empty() (in module AFQ.recognition.recognize) _roi_transform_helper() (AFQ.api.bundle_dict.BundleDict method) _run_chunk_local() (in module AFQ.recognition.criteria) _run_global_phase() (in module AFQ.recognition.criteria) _to_color_range() (in module AFQ.viz.plotly_backend) _use_bids_info() (AFQ.api.bundle_dict.BundleDict method) _validate_criteria() (in module AFQ.recognition.criteria) _viz_prepare_vol() (in module AFQ.tasks.viz)

A

affine_kwargs (AFQ.definitions.mapping.AffMap attribute) (AFQ.definitions.mapping.SynMap attribute) AffMap (class in AFQ.definitions.mapping) AFQ module AFQ.api module AFQ.api.bundle_dict module AFQ.api.group module AFQ.api.participant module AFQ.api.utils module AFQ.data module AFQ.data.fetch module AFQ.data.utils module AFQ.definitions module AFQ.definitions.image module AFQ.definitions.mapping module AFQ.definitions.utils module AFQ.models module AFQ.models.asym_filtering module AFQ.models.csd module AFQ.models.dki module AFQ.models.dti module AFQ.models.fwdti module AFQ.models.msmt module AFQ.models.QBallTP module AFQ.models.wmgm_interface module AFQ.nn module AFQ.nn.brainchop module AFQ.nn.multiaxial module AFQ.nn.synthseg module AFQ.nn.utils module AFQ.recognition module AFQ.recognition.cleaning module AFQ.recognition.clustering module AFQ.recognition.criteria module AFQ.recognition.curvature module AFQ.recognition.other_bundles module AFQ.recognition.preprocess module AFQ.recognition.recognize module AFQ.recognition.roi module AFQ.recognition.sparse_decisions module

AFQ.recognition.utils module AFQ.registration module AFQ.tasks module AFQ.tasks.data module AFQ.tasks.decorators module AFQ.tasks.mapping module AFQ.tasks.segmentation module AFQ.tasks.structural module AFQ.tasks.tissue module AFQ.tasks.tractography module AFQ.tasks.utils module AFQ.tasks.viz module AFQ.tractography module AFQ.tractography.tractography module AFQ.tractography.utils module AFQ.utils module AFQ.utils.bin module AFQ.utils.docs module AFQ.utils.docstring_parser module AFQ.utils.models module AFQ.utils.path module AFQ.utils.stats module AFQ.utils.streamlines module AFQ.utils.volume module AFQ.viz module AFQ.viz.altair module AFQ.viz.fury_backend module AFQ.viz.plot module AFQ.viz.plotly_backend module AFQ.viz.utils module AFQclass_doc (in module AFQ.api.utils), [1] altair_color_dict() (in module AFQ.viz.altair) altair_df_to_chart() (in module AFQ.viz.altair) anisotropic_index() (in module AFQ.models.QBallTP) anisotropic_power_map() (in module AFQ.tasks.data) apply_cmd_to_afq_derivs() (in module AFQ.utils.path) apply_conditions() (AFQ.definitions.image.LabelledImageFile method) apply_to_rois() (AFQ.api.bundle_dict.BundleDict method) as_file() (in module AFQ.tasks.decorators) as_fit_deriv() (in module AFQ.tasks.decorators) as_img() (in module AFQ.tasks.decorators) assemble_AFQ_browser() (AFQ.api.group.GroupAFQ method) aws_import_msg_error() (in module AFQ.data.utils) Axes (class in AFQ.viz.plotly_backend) axes_dict (in module AFQ.recognition.utils)

B

b0() (in module AFQ.tasks.data) b0_mask() (in module AFQ.tasks.data) b_name (AFQ.recognition.utils.SlsBeingRecognized attribute) baby_bd() (in module AFQ.api.bundle_dict) backend (AFQ.viz.utils.Viz attribute) BACKGROUND (AFQ.nn.synthseg.SynthSegLabels attribute) BACKGROUND_PARC (AFQ.nn.synthseg.SynthSegLabels attribute)

brain_mask() (in module AFQ.tasks.data) BRAIN_STEM (AFQ.nn.synthseg.SynthSegLabels attribute) bundle_idxs (AFQ.utils.streamlines.SegmentedSFT attribute) BUNDLE_MAT_2_PYTHON (in module AFQ.data.utils) bundle_names (AFQ.api.bundle_dict.BundleDict attribute) (AFQ.utils.streamlines.SegmentedSFT attribute) BUNDLE_RECO_2_AFQ (in module AFQ.data.utils) BundleDict (class in AFQ.api.bundle_dict)

C

callosal_bd() (in module AFQ.api.bundle_dict) cerebellar_bd() (in module AFQ.api.bundle_dict) check_sl_with_exclusion() (in module AFQ.recognition.roi) check_sls_with_inclusion() (in module AFQ.recognition.roi) chunk_indices() (in module AFQ.utils.stats) citations (AFQ.api.bundle_dict.BundleDict attribute) citations() (in module AFQ.tasks.viz) clean_bundle() (in module AFQ.recognition.cleaning) clean_by_endpoints() (in module AFQ.recognition.roi) clean_by_isolation_forest() (in module AFQ.recognition.cleaning) clean_by_orientation() (in module AFQ.recognition.cleaning) clean_by_orientation_mahalanobis() (in module AFQ.recognition.cleaning) clean_by_other_bundle() (in module AFQ.recognition.criteria) clean_by_overlap() (in module AFQ.recognition.other_bundles) clean_relative_to_other_core() (in module AFQ.recognition.other_bundles) clobber (AFQ.api.group.GroupAFQ attribute) (AFQ.api.participant.ParticipantAFQ attribute) cmd_outputs() (AFQ.api.group.GroupAFQ method) (AFQ.api.participant.ParticipantAFQ method) combine_bundle() (AFQ.api.group.GroupAFQ method) combine_profiles() (AFQ.api.group.GroupAFQ method) combined_profiles_df_to_altair_df() (in module AFQ.viz.altair) compute_asymmetry_index() (in module AFQ.models.asym_filtering) compute_nufid_asym() (in module AFQ.models.asym_filtering) compute_odd_power_map() (in module AFQ.models.asym_filtering) compute_sparse_decisions() (in module AFQ.recognition.sparse_decisions) configure_ncpus_nthreads() (in module AFQ.tasks.structural) contrast_index() (in module AFQ.utils.stats) copy() (AFQ.api.bundle_dict.BundleDict method) (AFQ.recognition.utils.SlsBeingRecognized method) create_gif() (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend) criteria_order_chunk_local (in module AFQ.recognition.criteria) criteria_order_post_other_bundles (in module AFQ.recognition.criteria) criteria_order_pre_other_bundles (in module AFQ.recognition.criteria) crop_to_nonzero() (in module AFQ.nn.utils) cross_midline() (in module AFQ.recognition.criteria) crosses (AFQ.recognition.preprocess.PreprocPlan property) csa_ai() (in module AFQ.tasks.data) csa_params() (in module AFQ.tasks.data) csa_pmap() (in module AFQ.tasks.data) csd_anisotropic_index() (in module AFQ.tasks.data) csd_aodf() (in module AFQ.tasks.data) csd_aodf_asi() (in module AFQ.tasks.data) csd_aodf_nufid() (in module AFQ.tasks.tissue) csd_aodf_opm() (in module AFQ.tasks.data) csd_params() (in module AFQ.tasks.data) CSF (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_BANKSSTS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_CAUDALANTERIORCINGULATE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_CAUDALMIDDLEFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_CUNEUS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_ENTORHINAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_FRONTALPOLE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_FUSIFORM (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_INFERIORPARIETAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_INFERIORTEMPORAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_INSULA (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_ISTHMUSCINGULATE (AFQ.nn.synthseg.SynthSegLabels attribute)

CTX_LH_LATERALOCCIPITAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_LATERALORBITOFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_LINGUAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_MEDIALORBITOFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_MIDDLETEMPORAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_PARACENTRAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_PARAHIPPOCAMPAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_PARSOPERCULARIS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_PARSORBITALIS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_PARSTRIANGULARIS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_PERICALCARINE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_POSTCENTRAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_POSTERIORCINGULATE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_PRECENTRAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_PRECUNEUS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_ROSTRALANTERIORCINGULATE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_ROSTRALMIDDLEFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_SUPERIORFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_SUPERIORPARIETAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_SUPERIORTEMPORAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_SUPRAMARGINAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_TEMPORALPOLE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_LH_TRANSVERSETEMPORAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_BANKSSTS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_CAUDALANTERIORCINGULATE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_CAUDALMIDDLEFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_CUNEUS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_ENTORHINAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_FRONTALPOLE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_FUSIFORM (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_INFERIORPARIETAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_INFERIORTEMPORAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_INSULA (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_ISTHMUSCINGULATE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_LATERALOCCIPITAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_LATERALORBITOFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_LINGUAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_MEDIALORBITOFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_MIDDLETEMPORAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_PARACENTRAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_PARAHIPPOCAMPAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_PARSOPERCULARIS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_PARSORBITALIS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_PARSTRIANGULARIS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_PERICALCARINE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_POSTCENTRAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_POSTERIORCINGULATE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_PRECENTRAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_PRECUNEUS (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_ROSTRALANTERIORCINGULATE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_ROSTRALMIDDLEFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_SUPERIORFRONTAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_SUPERIORPARIETAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_SUPERIORTEMPORAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_SUPRAMARGINAL (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_TEMPORALPOLE (AFQ.nn.synthseg.SynthSegLabels attribute) CTX_RH_TRANSVERSETEMPORAL (AFQ.nn.synthseg.SynthSegLabels attribute) curvature() (in module AFQ.recognition.criteria) custom_tractography() (in module AFQ.tasks.tractography) cut_sls_by_closest() (in module AFQ.recognition.utils)

D

default_bd() (in module AFQ.api.bundle_dict) Definition (class in AFQ.definitions.utils) density_map() (in module AFQ.utils.volume) dice_coeff() (in module AFQ.utils.volume) dict_to_json() (in module AFQ.utils.bin) dict_to_toml() (in module AFQ.utils.bin) dilate (AFQ.definitions.image.RoiImage attribute) DIPY_GH (in module AFQ.tasks.data) dki_ad() (in module AFQ.tasks.data) dki_ak() (in module AFQ.tasks.data) dki_awf() (in module AFQ.tasks.data) dki_cfa() (in module AFQ.tasks.data) dki_cl() (in module AFQ.tasks.data) dki_cp() (in module AFQ.tasks.data) dki_cs() (in module AFQ.tasks.data) dki_fa() (in module AFQ.tasks.data) dki_fit() (in module AFQ.tasks.data) dki_ga() (in module AFQ.tasks.data)

dki_kfa() (in module AFQ.tasks.data) dki_kt() (in module AFQ.tasks.data) dki_lt() (in module AFQ.tasks.data) dki_md() (in module AFQ.tasks.data) dki_mk() (in module AFQ.tasks.data) dki_params() (in module AFQ.tasks.data) dki_rd() (in module AFQ.tasks.data) dki_rk() (in module AFQ.tasks.data) drop_extension() (in module AFQ.utils.path) dti_ad() (in module AFQ.tasks.data) dti_cfa() (in module AFQ.tasks.data) dti_fa() (in module AFQ.tasks.data) dti_fit() (in module AFQ.tasks.data) dti_ga() (in module AFQ.tasks.data) dti_lt() (in module AFQ.tasks.data) dti_md() (in module AFQ.tasks.data) dti_params() (in module AFQ.tasks.data) dti_pdd() (in module AFQ.tasks.data) dti_rd() (in module AFQ.tasks.data)

E

end() (in module AFQ.recognition.criteria) endpoint_dists (AFQ.recognition.preprocess.PreprocPlan property) endpoint_dists() (in module AFQ.recognition.criteria) exclude() (in module AFQ.recognition.criteria) exclusive_labels (AFQ.definitions.image.LabelledImageFile attribute) export() (AFQ.api.group.GroupAFQ method) (AFQ.api.participant.ParticipantAFQ method) export_all() (AFQ.api.group.GroupAFQ method) (AFQ.api.participant.ParticipantAFQ method) export_bundle_lengths() (in module AFQ.tasks.segmentation)

export_bundles() (in module AFQ.tasks.segmentation) export_density_maps() (in module AFQ.tasks.segmentation) export_group_density() (AFQ.api.group.GroupAFQ method) export_registered_b0() (in module AFQ.tasks.mapping) export_rois() (in module AFQ.tasks.mapping) export_selected() (AFQ.recognition.utils.SlsBeingRecognized method) export_sl_counts() (in module AFQ.tasks.segmentation) export_up_to() (AFQ.api.group.GroupAFQ method) (AFQ.api.participant.ParticipantAFQ method) extract_brain_mask() (in module AFQ.nn.multiaxial)

F

fetch_brainchop_models (in module AFQ.data.fetch) fetch_callosum_templates (in module AFQ.data.fetch) fetch_multiaxial_models (in module AFQ.data.fetch) fetch_or_templates (in module AFQ.data.fetch) fetch_stanford_hardi_lv1 (in module AFQ.data.fetch) fetch_stanford_hardi_tractography (in module AFQ.data.fetch) fetch_synthseg_models (in module AFQ.data.fetch) fetch_templates (in module AFQ.data.fetch) fgarray (AFQ.recognition.preprocess.PreprocPlan property) find_file() (in module AFQ.definitions.utils) find_path() (AFQ.definitions.image.ImageFile method) (AFQ.definitions.image.PVEImages method) (AFQ.definitions.mapping.FnirtMap method) (AFQ.definitions.utils.Definition method) fit_csd() (in module AFQ.models.csd) fit_dki() (in module AFQ.models.dki)

fit_dti() (in module AFQ.models.dti) fit_fwdti() (in module AFQ.models.fwdti) fit_wm_gm_interface() (in module AFQ.models.wmgm_interface) flip_sls() (in module AFQ.recognition.utils) FnirtMap (class in AFQ.definitions.mapping) FOURTH_VENTRICLE (AFQ.nn.synthseg.SynthSegLabels attribute) from_qsiprep() (AFQ.api.group.GroupAFQ class method) from_selected() (AFQ.recognition.utils.SlsBeingRecognized class method) fromfile() (AFQ.utils.streamlines.SegmentedSFT class method) FullImage (class in AFQ.definitions.image) func_dict_to_arg_dict() (in module AFQ.utils.bin) fwdti_fa() (in module AFQ.tasks.data) fwdti_fit() (in module AFQ.tasks.data) fwdti_fwf() (in module AFQ.tasks.data) fwdti_md() (in module AFQ.tasks.data) fwdti_params() (in module AFQ.tasks.data)

G

gen_mapping() (AFQ.definitions.mapping.AffMap method) (AFQ.definitions.mapping.IdentityMap method) (AFQ.definitions.mapping.SlrMap method) gen_seeds() (in module AFQ.tractography.utils) generate_config() (in module AFQ.utils.bin) generate_json() (in module AFQ.utils.bin) get_b_info() (AFQ.api.bundle_dict.BundleDict method) get_base_fname() (in module AFQ.tasks.utils) get_bundle() (AFQ.utils.streamlines.SegmentedSFT method) get_bundle_dict() (in module AFQ.tasks.data) get_bundle_param_info() (AFQ.utils.streamlines.SegmentedSFT method) get_conflict_count() (in module AFQ.recognition.sparse_decisions) get_data_gtab() (in module AFQ.tasks.data) get_data_plan() (in module AFQ.tasks.data) get_fname() (in module AFQ.tasks.utils) get_for_subses() (AFQ.definitions.mapping.FnirtMap method) (AFQ.definitions.mapping.SynMap method) get_image_getter() (AFQ.definitions.image.FullImage method) (AFQ.definitions.image.ImageFile method) (AFQ.definitions.image.PVEImage method) (AFQ.definitions.image.PVEImages method) (AFQ.definitions.image.RoiImage method) (AFQ.definitions.image.ScalarImage method) (AFQ.definitions.image.TemplateImage method)

get_mapping_plan() (in module AFQ.tasks.mapping) get_name() (AFQ.definitions.image.FullImage method) (AFQ.definitions.image.ImageFile method) (AFQ.definitions.image.PVEImages method) (AFQ.definitions.image.RoiImage method) (AFQ.definitions.image.ScalarImage method) (AFQ.definitions.image.TemplateImage method) get_path_data_affine() (AFQ.definitions.image.ImageFile method) get_percentile_threshold() (in module AFQ.tractography.utils) get_reg_subject() (in module AFQ.tasks.mapping) get_scalar_dict() (in module AFQ.tasks.segmentation) get_segmentation_plan() (in module AFQ.tasks.segmentation) get_selected_sls() (AFQ.recognition.utils.SlsBeingRecognized method) get_streamlines_json() (AFQ.api.group.GroupAFQ method) get_structural_plan() (in module AFQ.tasks.structural) get_tissue_plan() (in module AFQ.tasks.tissue) get_tp() (in module AFQ.tasks.utils) get_tractography_plan() (in module AFQ.tasks.tractography) get_viz_plan() (in module AFQ.tasks.viz) GIFScraper (class in AFQ.utils.docs) gq() (in module AFQ.tasks.data) group_montage() (AFQ.api.group.GroupAFQ method) GroupAFQ (class in AFQ.api.group)

H

has_trx (in module AFQ.tasks.segmentation) (in module AFQ.utils.streamlines)

I

IdentityMap (class in AFQ.definitions.mapping) ImageFile (class in AFQ.definitions.image) include() (in module AFQ.recognition.criteria) inclusive_labels (AFQ.definitions.image.LabelledImageFile attribute)

init_viz_backend() (in module AFQ.tasks.viz) initiate_selection() (AFQ.recognition.utils.SlsBeingRecognized method) is_bundle_in_template() (AFQ.api.bundle_dict.BundleDict method) isolation_forest() (in module AFQ.recognition.criteria)

K

keep_in_memory (AFQ.api.bundle_dict.BundleDict attribute) kwargs (AFQ.api.group.GroupAFQ attribute) (AFQ.api.participant.ParticipantAFQ attribute)

kwargs_descriptors (in module AFQ.api.utils)

L

LabelledImageFile (class in AFQ.definitions.image) LEFT_ACCUMBENS_AREA (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_AMYGDALA (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_CAUDATE (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_CEREBELLUM_CORTEX (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_CEREBELLUM_WHITE_MATTER (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_CEREBRAL_CORTEX (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_CEREBRAL_WHITE_MATTER (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_HIPPOCAMPUS (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_HYPOTHALAMUS (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_INFERIOR_LATERAL_VENTRICLE (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_LATERAL_VENTRICLE (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_PALLIDUM (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_PUTAMEN (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_THALAMUS (AFQ.nn.synthseg.SynthSegLabels attribute) LEFT_VENTRAL_DC (AFQ.nn.synthseg.SynthSegLabels attribute) length() (in module AFQ.recognition.criteria)

lengths (AFQ.recognition.preprocess.PreprocPlan property) logger (AFQ.api.bundle_dict.BundleDict attribute) (AFQ.api.group.GroupAFQ attribute) (AFQ.api.participant.ParticipantAFQ attribute) (in module AFQ.recognition.cleaning) (in module AFQ.recognition.criteria) (in module AFQ.recognition.other_bundles) (in module AFQ.recognition.recognize) (in module AFQ.tasks.data) (in module AFQ.tasks.mapping) (in module AFQ.tasks.segmentation) (in module AFQ.tasks.structural) (in module AFQ.tasks.tissue) (in module AFQ.tasks.tractography) (in module AFQ.tasks.viz) (in module AFQ.tractography.utils) (in module AFQ.utils.volume)

M

mahalanobis() (in module AFQ.recognition.criteria) make_all_participant_montages() (AFQ.api.group.GroupAFQ method) make_workflow() (AFQ.api.participant.ParticipantAFQ method) manual_orient_sls() (in module AFQ.recognition.utils) mapping() (in module AFQ.tasks.mapping) methods_descriptors (in module AFQ.api.utils) model_input_parser() (in module AFQ.utils.bin) model_predict_input_parser() (in module AFQ.utils.bin) module AFQ AFQ.api AFQ.api.bundle_dict AFQ.api.group AFQ.api.participant AFQ.api.utils AFQ.data AFQ.data.fetch AFQ.data.utils AFQ.definitions AFQ.definitions.image AFQ.definitions.mapping AFQ.definitions.utils AFQ.models AFQ.models.asym_filtering AFQ.models.csd AFQ.models.dki AFQ.models.dti AFQ.models.fwdti AFQ.models.msmt AFQ.models.QBallTP AFQ.models.wmgm_interface AFQ.nn AFQ.nn.brainchop AFQ.nn.multiaxial AFQ.nn.synthseg AFQ.nn.utils AFQ.recognition AFQ.recognition.cleaning AFQ.recognition.clustering AFQ.recognition.criteria AFQ.recognition.curvature AFQ.recognition.other_bundles AFQ.recognition.preprocess AFQ.recognition.recognize AFQ.recognition.roi AFQ.recognition.sparse_decisions AFQ.recognition.utils AFQ.registration AFQ.tasks AFQ.tasks.data AFQ.tasks.decorators AFQ.tasks.mapping AFQ.tasks.segmentation AFQ.tasks.structural AFQ.tasks.tissue AFQ.tasks.tractography AFQ.tasks.utils AFQ.tasks.viz AFQ.tractography AFQ.tractography.tractography AFQ.tractography.utils AFQ.utils AFQ.utils.bin AFQ.utils.docs AFQ.utils.docstring_parser AFQ.utils.models AFQ.utils.path AFQ.utils.stats AFQ.utils.streamlines AFQ.utils.volume AFQ.viz AFQ.viz.altair AFQ.viz.fury_backend AFQ.viz.plot AFQ.viz.plotly_backend AFQ.viz.utils

move_streamlines() (in module AFQ.utils.streamlines) msdki_fit() (in module AFQ.tasks.data) msdki_msd() (in module AFQ.tasks.data) msdki_msk() (in module AFQ.tasks.data) msdki_params() (in module AFQ.tasks.data) msmt_aodf() (in module AFQ.tasks.tissue) msmt_aodf_asi() (in module AFQ.tasks.tissue) msmt_aodf_nufid() (in module AFQ.tasks.tissue) msmt_aodf_opm() (in module AFQ.tasks.tissue) msmt_apm() (in module AFQ.tasks.tissue) msmt_params() (in module AFQ.tasks.tissue) multiaxial() (in module AFQ.nn.multiaxial) mx_model() (in module AFQ.tasks.structural)

N

n_roi (AFQ.recognition.utils.SlsBeingRecognized attribute)

name_from_path() (in module AFQ.definitions.utils)

O

og_kwargs (AFQ.api.participant.ParticipantAFQ attribute) only_wm (AFQ.definitions.image.RoiImage attribute) only_wmgmi (AFQ.definitions.image.RoiImage attribute) onnx_kwargs() (in module AFQ.tasks.structural) opdt_ai() (in module AFQ.tasks.data)

opdt_params() (in module AFQ.tasks.data) opdt_pmap() (in module AFQ.tasks.data) organize_stanford_data() (in module AFQ.data.fetch) orient_by_streamline() (in module AFQ.recognition.utils) orient_mahal() (in module AFQ.recognition.criteria) oriented_yet (AFQ.recognition.utils.SlsBeingRecognized attribute)

P

pAFQ_inputs_list (AFQ.api.group.GroupAFQ attribute) pAFQ_list (AFQ.api.group.GroupAFQ attribute) parallel_params (AFQ.api.group.GroupAFQ attribute) parse_config_run_afq() (in module AFQ.utils.bin) parse_numpy_docstring() (in module AFQ.utils.docstring_parser) participant_montage() (AFQ.api.participant.ParticipantAFQ method) ParticipantAFQ (class in AFQ.api.participant) path (AFQ.definitions.image.TemplateImage attribute) plans_dict (AFQ.api.group.GroupAFQ attribute) plot_tract_profiles() (in module AFQ.tasks.viz) PNGScraper (class in AFQ.utils.docs) predict() (in module AFQ.models.dki) (in module AFQ.models.dti)

prepare_data() (in module AFQ.utils.models) prepare_t1_for_nn() (in module AFQ.nn.utils) PreprocPlan (class in AFQ.recognition.preprocess) primary_axis() (in module AFQ.recognition.criteria) prob_map() (in module AFQ.recognition.criteria) probsegs (AFQ.definitions.image.PVEImages attribute) pve_internal() (in module AFQ.tasks.tissue) pve_order (AFQ.definitions.image.PVEImage attribute) PVEImage (class in AFQ.definitions.image) PVEImages (class in AFQ.definitions.image) pyafq_str_to_val() (in module AFQ.utils.bin)

Q

qb_thresh() (in module AFQ.recognition.criteria)

qsi_prep_ignore_params (in module AFQ.utils.bin)

R

read_affine_mapping() (in module AFQ.registration) read_callosum_templates() (in module AFQ.data.fetch) read_json() (in module AFQ.utils.path) read_old_mapping() (in module AFQ.registration) read_or_templates() (in module AFQ.data.fetch) read_stanford_hardi_tractography() (in module AFQ.data.fetch) read_syn_mapping() (in module AFQ.registration) read_templates() (in module AFQ.data.fetch) reco_bd() (in module AFQ.api.bundle_dict) recobundles() (in module AFQ.recognition.criteria) recognize() (in module AFQ.recognition.recognize) recognize_bundles() (in module AFQ.recognition.criteria) ref (AFQ.recognition.utils.SlsBeingRecognized attribute) ref_sls (AFQ.recognition.utils.SlsBeingRecognized attribute) relax_cleaning() (AFQ.api.bundle_dict.BundleDict method) remove_conflicts() (in module AFQ.recognition.sparse_decisions) reorient() (AFQ.recognition.utils.SlsBeingRecognized method) resample (AFQ.definitions.image.ImageFile attribute) resample_output() (in module AFQ.nn.utils) resample_subject_to (AFQ.api.bundle_dict.BundleDict attribute) resample_tg() (in module AFQ.recognition.utils)

resample_to (AFQ.api.bundle_dict.BundleDict attribute) RIGHT_ACCUMBENS_AREA (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_AMYGDALA (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_CAUDATE (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_CEREBELLUM_CORTEX (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_CEREBELLUM_WHITE_MATTER (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_CEREBRAL_CORTEX (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_CEREBRAL_WHITE_MATTER (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_HIPPOCAMPUS (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_HYPOTHALAMUS (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_INFERIOR_LATERAL_VENTRICLE (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_LATERAL_VENTRICLE (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_PALLIDUM (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_PUTAMEN (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_THALAMUS (AFQ.nn.synthseg.SynthSegLabels attribute) RIGHT_VENTRAL_DC (AFQ.nn.synthseg.SynthSegLabels attribute) RoiImage (class in AFQ.definitions.image) rumba_params() (in module AFQ.tasks.data) run_brainchop() (in module AFQ.nn.brainchop) run_multiaxial() (in module AFQ.nn.multiaxial) run_synthseg() (in module AFQ.nn.synthseg)

S

save_intermediates (AFQ.recognition.utils.SlsBeingRecognized attribute) scalar (AFQ.definitions.image.ScalarImage attribute) (AFQ.definitions.image.ThresholdedScalarImage attribute) ScalarImage (class in AFQ.definitions.image) scene_rotate_forward() (in module AFQ.viz.fury_backend) scope (in module AFQ.viz.plotly_backend) seen (AFQ.utils.docs.GIFScraper attribute) (AFQ.utils.docs.PNGScraper attribute) segment() (in module AFQ.tasks.segmentation) SegmentedSFT (class in AFQ.utils.streamlines) select() (AFQ.recognition.utils.SlsBeingRecognized method) selected_fiber_idxs (AFQ.recognition.utils.SlsBeingRecognized attribute) sessions (AFQ.api.group.GroupAFQ attribute) set_layout() (in module AFQ.viz.plotly_backend) sft (AFQ.utils.streamlines.SegmentedSFT attribute) sidecar_info (AFQ.utils.streamlines.SegmentedSFT attribute) single_bundle_viz() (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend) sl_curve() (in module AFQ.recognition.curvature)

sl_curve_dist() (in module AFQ.recognition.curvature) slr_kwargs (AFQ.definitions.mapping.SlrMap attribute) SlrMap (class in AFQ.definitions.mapping) sls_flipped (AFQ.recognition.utils.SlsBeingRecognized attribute) sls_mapping() (in module AFQ.tasks.mapping) SlsBeingRecognized (class in AFQ.recognition.utils) space_from_fname() (in module AFQ.utils.path) spectral_atlas_label() (in module AFQ.recognition.clustering) split_streamline() (in module AFQ.utils.streamlines) start() (in module AFQ.recognition.criteria) start_time (AFQ.recognition.utils.SlsBeingRecognized attribute) str_for_toml() (AFQ.definitions.utils.Definition method) streamlines() (in module AFQ.tasks.tractography) subcluster_by_atlas() (in module AFQ.recognition.clustering) subjects (AFQ.api.group.GroupAFQ attribute) syn_kwargs (AFQ.definitions.mapping.SynMap attribute) SynMap (class in AFQ.definitions.mapping) synthseg_model() (in module AFQ.tasks.structural) SynthSegLabels (class in AFQ.nn.synthseg)

T

t1_masked() (in module AFQ.tasks.structural) t1_subcortex() (in module AFQ.tasks.structural) t1w_brain_mask() (in module AFQ.tasks.structural) t1w_over_b0() (in module AFQ.tasks.data) template_xform() (in module AFQ.tasks.mapping) TemplateImage (class in AFQ.definitions.image) tg (AFQ.recognition.preprocess.PreprocPlan attribute) THIRD_VENTRICLE (AFQ.nn.synthseg.SynthSegLabels attribute) ThresholdedImageFile (class in AFQ.definitions.image)

ThresholdedScalarImage (class in AFQ.definitions.image) tissue_property (AFQ.definitions.image.RoiImage attribute) tissue_property_n_voxel (AFQ.definitions.image.RoiImage attribute) tissue_property_threshold (AFQ.definitions.image.RoiImage attribute) tolerance_mm_to_vox() (in module AFQ.recognition.utils) track() (in module AFQ.tractography.tractography) tract_profiles() (in module AFQ.tasks.segmentation) transform_roi() (in module AFQ.utils.volume) transform_rois() (AFQ.api.bundle_dict.BundleDict method)

U

unified_filtering() (in module AFQ.models.asym_filtering) upload_to_s3() (AFQ.api.group.GroupAFQ method) use_endpoints (AFQ.definitions.image.RoiImage attribute)

use_prealign (AFQ.definitions.mapping.SynMap attribute) use_presegment (AFQ.definitions.image.RoiImage attribute) use_waypoints (AFQ.definitions.image.RoiImage attribute)

V

val_to_toml() (in module AFQ.utils.bin) valid_noncriterion (in module AFQ.recognition.criteria) valid_ses_list (AFQ.api.group.GroupAFQ attribute) valid_sub_list (AFQ.api.group.GroupAFQ attribute) visualize_bundles() (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend) visualize_gif_inline() (in module AFQ.viz.plot) visualize_roi() (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend)

visualize_tract_profiles() (in module AFQ.viz.plot) visualize_volume() (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend) Viz (class in AFQ.viz.utils) viz_bundles() (in module AFQ.tasks.viz) viz_indivBundle() (in module AFQ.tasks.viz) viz_logger (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend)

W

with_name() (in module AFQ.tasks.utils)

wm_gm_interface() (in module AFQ.tasks.tissue) write_json() (in module AFQ.utils.path)

X

X (AFQ.viz.plotly_backend.Axes attribute)

Y

Y (AFQ.viz.plotly_backend.Axes attribute)

Z

Z (AFQ.viz.plotly_backend.Axes attribute)