Index

_

__add__() (AFQ.api.bundle_dict.BundleDict method) __bool__() (AFQ.recognition.utils.SlsBeingRecognized method) __call__() (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) __repr__() (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) _cond_load() (AFQ.api.bundle_dict.BundleDict method) _cond_load_bundle() (AFQ.api.bundle_dict.BundleDict method) _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) _ga_id (in module AFQ) _gen_seeds() (in module AFQ.tasks.tractography) _inline_interact() (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend) _meta_from_tracking_params() (in module AFQ.tasks.tractography) _name_from_enum() (in module AFQ.viz.plotly_backend) _plot_profiles() (in module AFQ.viz.plotly_backend) _return_empty() (in module AFQ.recognition.recognize) _roi_transform_helper() (AFQ.api.bundle_dict.BundleDict method) _to_color_range() (in module AFQ.viz.plotly_backend) _tracking() (in module AFQ.tractography.tractography) _use_bids_info() (AFQ.api.bundle_dict.BundleDict method) _viz_prepare_vol() (in module AFQ.tasks.viz)

A

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.csd module AFQ.models.dki module AFQ.models.dti module AFQ.models.fwdti module AFQ.models.QBallTP module AFQ.recognition module AFQ.recognition.cleaning module AFQ.recognition.criteria module AFQ.recognition.curvature module AFQ.recognition.preprocess module AFQ.recognition.recognize module AFQ.recognition.roi 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.tractography module AFQ.tasks.utils module AFQ.tasks.viz module AFQ.tractography module AFQ.tractography.gputractography module AFQ.tractography.tractography module AFQ.tractography.utils module AFQ.utils module AFQ.utils.bin module AFQ.utils.docs 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.ImageFile method) (AFQ.definitions.image.LabelledImageFile method) (AFQ.definitions.image.ThresholdedImageFile 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) Axes (class in AFQ.viz.plotly_backend)

B

b0() (in module AFQ.tasks.data) b0_mask() (in module AFQ.tasks.data) B0Image (class in AFQ.definitions.image) baby_bd() (in module AFQ.api.bundle_dict)

brain_mask() (in module AFQ.tasks.data) bundle_criterion_order (in module AFQ.recognition.criteria) BUNDLE_MAT_2_PYTHON (in module AFQ.data.utils) 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_sl_with_inclusion() (in module AFQ.recognition.roi) check_sls_with_inclusion() (in module AFQ.recognition.roi) clean_bundle() (in module AFQ.recognition.cleaning) clean_by_endpoints() (in module AFQ.recognition.roi) clean_by_orientation() (in module AFQ.recognition.cleaning) 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) contrast_index() (in module AFQ.utils.stats) copy() (AFQ.api.bundle_dict.BundleDict method) create_gif() (in module AFQ.viz.fury_backend) (in module AFQ.viz.plotly_backend) cross_midline() (in module AFQ.recognition.criteria) crosses() (in module AFQ.recognition.preprocess) 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_params() (in module AFQ.tasks.data) curvature() (in module AFQ.recognition.criteria) custom_tractography() (in module AFQ.tasks.tractography) cut_sls_by_dist() (in module AFQ.recognition.utils)

D

default18_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) 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_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) exclude() (in module AFQ.recognition.criteria) 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_seed_mask() (in module AFQ.tasks.tractography) export_sl_counts() (in module AFQ.tasks.segmentation) export_stop_mask() (in module AFQ.tasks.tractography) export_stop_mask_pft() (in module AFQ.tasks.tractography) export_up_to() (AFQ.api.group.GroupAFQ method) (AFQ.api.participant.ParticipantAFQ method) extract_odf() (in module AFQ.models.QBallTP)

F

fetch_callosum_templates (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_templates (in module AFQ.data.fetch) fgarray() (in module AFQ.recognition.preprocess) find_file() (in module AFQ.definitions.utils) find_path() (AFQ.definitions.image.ImageFile 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) flip_sls() (in module AFQ.recognition.utils) FnirtMap (class in AFQ.definitions.mapping) 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.SlrMap method) (AFQ.definitions.mapping.SynMap method) gen_seeds() (in module AFQ.tractography.utils) generate_config() (in module AFQ.utils.bin) generate_json() (in module AFQ.utils.bin) get_afq_bids_entities_fname() (in module AFQ.api.group) 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_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.IdentityMap method) get_image_getter() (AFQ.definitions.image.B0Image method) (AFQ.definitions.image.FullImage method) (AFQ.definitions.image.GQImage method) (AFQ.definitions.image.ImageFile 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.B0Image method) (AFQ.definitions.image.FullImage method) (AFQ.definitions.image.GQImage method) (AFQ.definitions.image.ImageFile 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_preproc_plan() (in module AFQ.recognition.preprocess) 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_sft_and_sidecar() (AFQ.utils.streamlines.SegmentedSFT method) get_streamlines_json() (AFQ.api.group.GroupAFQ method) get_tractography_plan() (in module AFQ.tasks.tractography) get_viz_plan() (in module AFQ.tasks.viz) gpu_track() (in module AFQ.tractography.gputractography) gpu_tractography() (in module AFQ.tasks.tractography) gq() (in module AFQ.tasks.data) gq_ai() (in module AFQ.tasks.data) gq_pmap() (in module AFQ.tasks.data) GQImage (class in AFQ.definitions.image) group_montage() (AFQ.api.group.GroupAFQ method) GroupAFQ (class in AFQ.api.group)

H

has_gputrack (in module AFQ.tasks.tractography) has_ray (in module AFQ.tasks.tractography)

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

I

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

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)

K

kwargs_descriptors (in module AFQ.api.utils)

L

LabelledImageFile (class in AFQ.definitions.image) length() (in module AFQ.recognition.criteria) logger (in module AFQ.recognition.cleaning) (in module AFQ.recognition.criteria) (in module AFQ.recognition.preprocess) (in module AFQ.recognition.recognize) (in module AFQ.recognition.utils) (in module AFQ.tasks.data) (in module AFQ.tasks.mapping) (in module AFQ.tasks.segmentation) (in module AFQ.tasks.tractography) (in module AFQ.tasks.viz) (in module AFQ.tractography.gputractography) (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) 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.csd AFQ.models.dki AFQ.models.dti AFQ.models.fwdti AFQ.models.QBallTP AFQ.recognition AFQ.recognition.cleaning AFQ.recognition.criteria AFQ.recognition.curvature AFQ.recognition.preprocess AFQ.recognition.recognize AFQ.recognition.roi AFQ.recognition.utils AFQ.registration AFQ.tasks AFQ.tasks.data AFQ.tasks.decorators AFQ.tasks.mapping AFQ.tasks.segmentation AFQ.tasks.tractography AFQ.tasks.utils AFQ.tasks.viz AFQ.tractography AFQ.tractography.gputractography AFQ.tractography.tractography AFQ.tractography.utils AFQ.utils AFQ.utils.bin AFQ.utils.docs 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.recognition.utils) 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)

N

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

O

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)

P

parse_config_run_afq() (in module AFQ.utils.bin) participant_montage() (AFQ.api.participant.ParticipantAFQ method) ParticipantAFQ (class in AFQ.api.participant) patch_up_roi() (in module AFQ.utils.volume) 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) primary_axis() (in module AFQ.recognition.criteria) prob_map() (in module AFQ.recognition.criteria)

Q

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

qsi_prep_ignore_params (in module AFQ.utils.bin)

R

read_callosum_templates() (in module AFQ.data.fetch) read_json() (in module AFQ.utils.path) read_mapping() (in module AFQ.registration) read_or_templates() (in module AFQ.data.fetch) read_stanford_hardi_tractography() (in module AFQ.data.fetch) read_templates() (in module AFQ.data.fetch) read_tg() (in module AFQ.recognition.utils) reco_bd() (in module AFQ.api.bundle_dict) recobundles() (in module AFQ.recognition.criteria) recognize() (in module AFQ.recognition.recognize)

reorient() (AFQ.recognition.utils.SlsBeingRecognized method) resample_tg() (in module AFQ.recognition.utils) RoiImage (class in AFQ.definitions.image) rumba_f_csf() (in module AFQ.tasks.data) rumba_f_gm() (in module AFQ.tasks.data) rumba_f_wm() (in module AFQ.tasks.data) rumba_fit() (in module AFQ.tasks.data) rumba_model() (in module AFQ.tasks.data) rumba_params() (in module AFQ.tasks.data) run_bundle_rec_plan() (in module AFQ.recognition.criteria)

S

ScalarImage (class in AFQ.definitions.image) scene_rotate_forward() (in module AFQ.viz.fury_backend) scope (in module AFQ.viz.plotly_backend) segment() (in module AFQ.tasks.segmentation) SegmentedSFT (class in AFQ.utils.streamlines) select() (AFQ.recognition.utils.SlsBeingRecognized method) set_layout() (in module AFQ.viz.plotly_backend) 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_registration() (in module AFQ.registration) SlrMap (class in AFQ.definitions.mapping) sls_mapping() (in module AFQ.tasks.mapping) SlsBeingRecognized (class in AFQ.recognition.utils) split_streamline() (in module AFQ.utils.streamlines) start() (in module AFQ.recognition.criteria) str_for_toml() (AFQ.definitions.utils.Definition method) streamlines() (in module AFQ.tasks.tractography) syn_register_dwi() (in module AFQ.registration) SynMap (class in AFQ.definitions.mapping)

T

template_xform() (in module AFQ.tasks.mapping) TemplateImage (class in AFQ.definitions.image) ThresholdedImageFile (class in AFQ.definitions.image) ThresholdedScalarImage (class in AFQ.definitions.image) tolerance_mm_to_vox() (in module AFQ.recognition.preprocess)

toml_to_val() (in module AFQ.utils.bin) track() (in module AFQ.tractography.tractography) tract_profiles() (in module AFQ.tasks.segmentation) transform_inverse_roi() (in module AFQ.utils.volume) transform_rois() (AFQ.api.bundle_dict.BundleDict method)

U

update_max_includes() (AFQ.api.bundle_dict.BundleDict method)

upload_to_s3() (AFQ.api.group.GroupAFQ method)

V

val_to_toml() (in module AFQ.utils.bin) 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)

write_json() (in module AFQ.utils.path) write_mapping() (in module AFQ.registration)

X

X (AFQ.viz.plotly_backend.Axes attribute)

Y

Y (AFQ.viz.plotly_backend.Axes attribute)

Z

Z (AFQ.viz.plotly_backend.Axes attribute)