Index

_

__getnewargs__() (ConditionInfo method) (ContrastInfo method) __getstate__() (ConditionInfo method) (ContrastInfo method)

__init__() (BaseReader method) __repr__() (ConditionInfo method) (ContrastInfo method)

A

abstract_test_lines_in_polyline() (in module braviz.readAndFilter.filter_fibers) AbstractPlot (class in braviz.visualization.matplotlib_qt_widget) active_bundles (TraculaManager attribute) actor (FmriContours attribute) add_bundle() (SimpleBundlesList method) add_child() (StructureTreeNode method) add_data_frame() (in module braviz.readAndFilter.tabular_data) add_filter() (SamplesFilterModel method) add_from_database() (TractographyManager method) add_interactor() (AnovaRegressorsModel method) add_interactor_by_names() (AnovaRegressorsModel method) add_label() (NominalVariablesMeta method) add_node() (LogicBundleQtTree method) add_regressor() (AnovaRegressorsModel method) add_son() (LogicBundleNode method) add_son_from_dict() (LogicBundleNode method) add_subjects() (AbstractPlot method)

add_variable() (ContextVariablesModel method) addImg() (SimpleVtkViewer method) AdditionalCursors (class in braviz.visualization.subject_viewer) addLabels() (persistentImagePlane method) addPolyData() (SimpleVtkViewer method) addScalars() (in module braviz.readAndFilter.surfer_input) aggregate_in_roi() (in module braviz.interaction.structure_metrics) AggregateInRoi (class in braviz.interaction.structure_metrics) AnovaRegressorsModel (class in braviz.interaction.qt_models) AnovaResultsModel (class in braviz.interaction.qt_models) apply_filters() (SamplesFilterModel method) apply_offset() (in module braviz.readAndFilter.surfer_input) applyTransform() (in module braviz.readAndFilter.transforms) are_variables_names_nominal() (in module braviz.readAndFilter.tabular_data) are_variables_names_real() (in module braviz.readAndFilter.tabular_data) are_variables_nominal() (in module braviz.readAndFilter.tabular_data) are_variables_real() (in module braviz.readAndFilter.tabular_data)

B

BaseReader (class in braviz.readAndFilter.base_reader) boundingBoxIntesection() (in module braviz.readAndFilter.filter_fibers) braviz.applications (module) braviz.applications.anova_task (module) braviz.applications.braviz_web_server (module) braviz.applications.build_roi (module) braviz.applications.calculate_descriptors (module) braviz.applications.check_reg_app (module) braviz.applications.correlations (module) braviz.applications.fmri_explorer (module) braviz.applications.import_comments (module) braviz.applications.lm_task (module) braviz.applications.logic_bundles (module) braviz.applications.measure_task (module) braviz.applications.parallel_coordinates (module) braviz.applications.parse_spss_file (module) braviz.applications.populate_cache (module) braviz.applications.sample_overview (module) braviz.applications.subject_overview (module) braviz.interaction (module) braviz.interaction.connection (module) braviz.interaction.descriptors (module) braviz.interaction.logic_bundle_model (module) braviz.interaction.qt_dialogs (module) braviz.interaction.qt_models (module) braviz.interaction.qt_structures_model (module) braviz.interaction.qt_widgets (module) braviz.interaction.r_functions (module) braviz.interaction.roi (module) braviz.interaction.structure_metrics (module) braviz.interaction.tornado_connection (module) braviz.readAndFilter (module)

braviz.readAndFilter.bundles_db (module) braviz.readAndFilter.cache (module) braviz.readAndFilter.check_db (module) braviz.readAndFilter.color_fibers (module) braviz.readAndFilter.config_file (module) braviz.readAndFilter.filter_fibers (module) braviz.readAndFilter.geom_db (module) braviz.readAndFilter.hierarchical_fibers (module) braviz.readAndFilter.images (module) braviz.readAndFilter.named_tracts (module) braviz.readAndFilter.read_csv (module) braviz.readAndFilter.read_spm (module) braviz.readAndFilter.readDartelTransform (module) braviz.readAndFilter.surfer_input (module) braviz.readAndFilter.tabular_data (module) braviz.readAndFilter.transforms (module) braviz.readAndFilter.user_data (module) braviz.visualization (module) braviz.visualization.checkerboard_view (module) braviz.visualization.d3_visualizations (module) braviz.visualization.fmri_view (module) braviz.visualization.matplotlib_qt_widget (module) braviz.visualization.simple_vtk (module) braviz.visualization.subject_viewer (module) braviz_auto_data_root() (in module braviz.readAndFilter) braviz_auto_dynamic_data_root() (in module braviz.readAndFilter) BravizAutoReader() (in module braviz.readAndFilter) BravizConfig (class in braviz.readAndFilter.config_file) broadcast_address (MessageServer attribute) build_grid() (in module braviz.visualization.simple_vtk) BundleSelectionDialog (class in braviz.interaction.qt_dialogs) BundlesSelectionList (class in braviz.interaction.qt_models)

C

cache (CacheContainer attribute) cache_function() (in module braviz.readAndFilter.cache) CacheContainer (class in braviz.readAndFilter.cache) cached_get_struct_metric_col() (in module braviz.interaction.structure_metrics) calculate_anova() (in module braviz.interaction.r_functions) calculate_gini_indexes() (VarAndGiniModel method) calculate_ginni_index() (in module braviz.interaction.r_functions) calculate_normalized_linear_regression() (in module braviz.interaction.r_functions) change_axis() (cursors method) change_color() (TractographyManager method) change_contrast() (fMRI_viewer method) change_current_space() (SubjectViewer method) change_image_modality() (ImageManager method) (MeasurerViewer method) (OrthogonalPlanesViewer method) change_image_orientation() (ImageManager method) change_orientation() (fMRI_viewer method) change_paradigm() (fMRI_viewer method) change_space() (CheckboardView method) (ImageManager method) (MeasurerViewer method) (OrthogonalPlanesViewer method) change_subject() (fMRI_viewer method) (ImageManager method) (MeasurerViewer method) (OrthogonalPlanesViewer method) (SubjectDetails method) (SubjectViewer method) check_and_update_tree() (StructureTreeNode method) check_if_name_exists() (in module braviz.readAndFilter.bundles_db) check_matrix() (in module braviz.readAndFilter.readDartelTransform) CheckboardView (class in braviz.visualization.checkerboard_view) checked (SubjectChecklist attribute) (SubjectCheckTable attribute) clear_cache_dir() (BaseReader method) clear_dynamic_data_dir() (BaseReader static method) clear_mem_cache() (BaseReader method) clear_poly_data() (SimpleVtkViewer method) clear_selection() (VarListModel method) CoefficientsPlot (class in braviz.visualization.matplotlib_qt_widget)

color_by_fa() (in module braviz.readAndFilter.color_fibers) color_by_z() (in module braviz.readAndFilter.color_fibers) color_fibers_lines() (in module braviz.readAndFilter.color_fibers) color_fibers_pts() (in module braviz.readAndFilter.color_fibers) column_to_vtk_array() (in module braviz.readAndFilter.read_csv) ConditionInfo (class in braviz.readAndFilter.read_spm) conditions (SpmFileReader attribute) connect_to_server() (GenericMessageClient method) (MessageClient method) (PassiveMessageClient method) ContextVariablesModel (class in braviz.interaction.qt_models) ContextVariablesPanel (class in braviz.interaction.qt_widgets) ContextVariablesSelectDialog (class in braviz.interaction.qt_dialogs) contours (fMRI_viewer attribute) (SubjectViewer attribute) ContrastInfo (class in braviz.readAndFilter.read_spm) contrasts (SpmFileReader attribute) copy_spheres() (in module braviz.readAndFilter.geom_db) corpus_callosum() (in module braviz.readAndFilter.named_tracts) cortex (OrthogonalPlanesViewer attribute) cortico_spinal_d() (in module braviz.readAndFilter.named_tracts) cortico_spinal_l() (in module braviz.readAndFilter.named_tracts) cortico_spinal_n() (in module braviz.readAndFilter.named_tracts) cortico_spinal_r() (in module braviz.readAndFilter.named_tracts) count_variable_scenarios() (in module braviz.readAndFilter.user_data) create_context_menu() (ContextVariablesPanel method) create_polydata() (in module braviz.readAndFilter.surfer_input) create_roi() (in module braviz.readAndFilter.geom_db) current_coords() (fMRI_viewer method) current_position() (OrthogonalPlanesViewer method) cursor_move_handler() (QFmriWidget method) cursors (class in braviz.visualization.simple_vtk)

D

dartel2GridTransform() (in module braviz.readAndFilter.readDartelTransform) dartel2GridTransform_cached() (in module braviz.readAndFilter.readDartelTransform) DataFrameModel (class in braviz.interaction.qt_models) decrease_son_number() (LogicBundleNode method) delete_children() (StructureTreeNode method) delete_sample() (in module braviz.readAndFilter.user_data) delete_scenario() (in module braviz.readAndFilter.user_data) design (ContrastInfo attribute) distance (MeasurerViewer attribute) distance_changed_handle() (QMeasurerWidget method) do_and_render() (in module braviz.visualization.subject_viewer)

does_variable_name_exists() (in module braviz.readAndFilter.tabular_data) draw_bars() (MatplotWidget method) draw_boxplot() (MatplotWidget method) draw_coefficients_plot() (MatplotWidget method) draw_histogram() (MatplotWidget method) draw_intercept() (MatplotWidget method) draw_message() (MatplotWidget method) draw_residuals() (MatplotWidget method) draw_scatter() (MatplotWidget method) draw_spider_plot() (MatplotWidget method) durations (ConditionInfo attribute)

E

emit_distance_changed_signal() (MeasurerViewer method) export_roi() (in module braviz.interaction.roi)

export_vars (module) extract_poly_data_subset() (in module braviz.readAndFilter.filter_fibers)

F

filter_bundle_with_sphere() (FilterBundleWithSphere method) filter_polylines_by_scalar() (in module braviz.readAndFilter.filter_fibers) filter_polylines_with_img() (in module braviz.readAndFilter.filter_fibers) filter_polylines_with_img_slow() (in module braviz.readAndFilter.filter_fibers) FilterArrows (class in braviz.visualization.subject_viewer) FilterBundleWithSphere (class in braviz.readAndFilter.filter_fibers)

filterPolylinesWithModel() (in module braviz.readAndFilter.filter_fibers) finish_initializing() (MeasurerViewer method) (OrthogonalPlanesViewer method) fMRI_blender (class in braviz.visualization.fmri_view) fMRI_viewer (class in braviz.visualization.subject_viewer) FmriContours (class in braviz.visualization.subject_viewer) from_dict() (LogicBundleNode static method)

G

generate_roi_image() (in module braviz.interaction.roi) GenericMessageClient (class in braviz.interaction.connection) GenericVariableSelectDialog (class in braviz.interaction.qt_dialogs) get() (BaseReader method) get_all_lines() (in module braviz.readAndFilter.hierarchical_fibers) get_all_spheres() (in module braviz.readAndFilter.geom_db) get_apps_config() (in module braviz.readAndFilter.config_file) get_arrow() (in module braviz.visualization.simple_vtk) get_auto_data_root() (BaseReader static method) get_auto_dyn_data_root() (BaseReader static method) get_auto_reader() (BaseReader static method) get_available_lines_df() (in module braviz.readAndFilter.geom_db) get_available_spheres_df() (in module braviz.readAndFilter.geom_db) get_background() (BravizConfig method) get_blended_img() (fMRI_blender method) get_bundle_colors() (TractographyManager method) get_bundle_details() (in module braviz.readAndFilter.bundles_db) get_bundle_ids_and_names() (in module braviz.readAndFilter.bundles_db) get_bundle_name() (in module braviz.readAndFilter.bundles_db) (SimpleBundlesList method) get_bundles_list() (in module braviz.readAndFilter.bundles_db) get_camera_parameters() (fMRI_viewer method) (MeasurerViewer method) (OrthogonalPlanesViewer method) (SubjectViewer method) get_checked() (NominalVariablesMeta method) get_column() (in module braviz.readAndFilter.read_csv) get_comment() (in module braviz.readAndFilter.user_data) get_condition_block() (SpmFileReader method) get_config() (in module braviz.readAndFilter.config_file) get_contrast_names() (SpmFileReader method) get_contrasts_dict() (in module braviz.readAndFilter.read_spm) get_coords() (AdditionalCursors method) get_current_column_indexes() (SubjectsTable method) get_current_columns() (SubjectsTable method) get_current_image_level() (ImageManager method) get_current_image_slice() (ImageManager method) get_current_image_window() (ImageManager method) get_current_slice() (MeasurerViewer method) (OrthogonalPlanesViewer method) get_current_variables() (SubjectDetails method) get_data_frame() (AnovaRegressorsModel method) get_data_frame_by_index() (in module braviz.readAndFilter.tabular_data) get_data_frame_by_name() (in module braviz.readAndFilter.tabular_data) get_data_root() (BaseReader method) get_default_subject() (BravizConfig method) get_default_variables() (BravizConfig method) get_descriptors() (in module braviz.interaction.descriptors) get_dyn_data_root() (BaseReader method) get_editables() (ContextVariablesPanel method) get_elements() (SimpleSetModel method) get_fa_lut() (in module braviz.readAndFilter.color_fibers) get_fiber_scalars_from_db() (in module braviz.interaction.structure_metrics) get_fiber_scalars_from_waypoints() (in module braviz.interaction.structure_metrics) get_fibers_metric() (in module braviz.interaction.structure_metrics) get_fmri_lut() (in module braviz.visualization.fmri_view) get_free_surfer_lut() (in module braviz.readAndFilter.surfer_input) get_headers() (in module braviz.readAndFilter.read_csv) get_host_config() (in module braviz.readAndFilter.config_file) get_ids() (SimpleBundlesList method) get_index() (ScenariosTableModel method) get_interaction_style() (BravizConfig method) get_interactions() (AnovaRegressorsModel method) get_interactors_dict() (AnovaRegressorsModel method) get_label() (persistentImagePlane method) get_labels_dict() (in module braviz.readAndFilter.tabular_data) get_labels_dict_by_name() (in module braviz.readAndFilter.tabular_data) get_last_id() (AbstractPlot method) get_last_message() (PassiveMessageClient method)

get_last_picked_pos() (SurfaceManager method) get_laterality() (BravizConfig method) (in module braviz.readAndFilter.tabular_data) get_leaf_names() (StructureTreeNode method) get_leafs() (SampleTree method) get_length_lut() (in module braviz.readAndFilter.color_fibers) get_logic_bundle_dict() (in module braviz.readAndFilter.bundles_db) get_maximum_value() (in module braviz.readAndFilter.tabular_data) get_min_max_opt_values_by_name() (in module braviz.readAndFilter.tabular_data) get_min_max_values() (in module braviz.readAndFilter.tabular_data) get_min_max_values_by_name() (in module braviz.readAndFilter.tabular_data) get_minimum_value() (in module braviz.readAndFilter.tabular_data) get_mult_struct_metric() (in module braviz.interaction.structure_metrics) get_name() (ScenariosTableModel method) get_node() (LogicBundleQtTree method) get_number_of_image_slices() (CheckboardView method) (ImageManager method) get_number_of_slices() (MeasurerViewer method) (OrthogonalPlanesViewer method) get_opacity() (ModelManager method) get_polydata() (TractographyManager method) get_position() (AdditionalCursors method) get_reference_population() (BravizConfig method) get_regressors() (AnovaRegressorsModel method) get_right_or_left_hemisphere() (in module braviz.interaction.structure_metrics) get_roi_id() (in module braviz.readAndFilter.geom_db) get_roi_name() (in module braviz.readAndFilter.geom_db) get_roi_space() (in module braviz.readAndFilter.geom_db) get_roi_type() (in module braviz.readAndFilter.geom_db) get_sample() (SamplesSelectionModel method) get_sample_data() (in module braviz.readAndFilter.user_data) get_sample_index() (SamplesSelectionModel method) get_sample_name() (SamplesSelectionModel method) get_samples_df() (in module braviz.readAndFilter.user_data) get_scalar_from_db() (TractographyManager method) get_scalar_from_fiber_ploydata() (in module braviz.interaction.structure_metrics) get_scalar_from_structs() (TractographyManager method) get_scalar_metrics() (ModelManager method) get_scenario_data_dict() (in module braviz.readAndFilter.user_data) get_scenarios_data_frame() (in module braviz.readAndFilter.user_data) get_selected() (BundlesSelectionList method) (SimpleCheckModel method) get_selected_structures() (StructureTreeModel method) get_show_color_bar() (TractographyManager method) get_struct_metric() (in module braviz.interaction.structure_metrics) get_subject_index() (SubjectsTable method) get_subject_variables() (in module braviz.readAndFilter.tabular_data) get_subjects() (in module braviz.readAndFilter.tabular_data) get_time_vector() (SpmFileReader method) get_tooltip() (AbstractPlot method) get_tuples_dict() (in module braviz.readAndFilter.read_csv) get_unchecked() (NominalVariablesMeta method) get_valid_lines_from_logical() (in module braviz.readAndFilter.hierarchical_fibers) get_valid_lines_from_node() (in module braviz.readAndFilter.hierarchical_fibers) get_valid_lines_from_roi() (in module braviz.readAndFilter.hierarchical_fibers) get_valid_lines_from_struct() (in module braviz.readAndFilter.hierarchical_fibers) get_value() (AggregateInRoi method) get_var_description() (in module braviz.readAndFilter.tabular_data) get_var_description_by_name() (in module braviz.readAndFilter.tabular_data) get_var_idx() (in module braviz.readAndFilter.tabular_data) get_var_name() (in module braviz.readAndFilter.tabular_data) get_var_value() (in module braviz.readAndFilter.tabular_data) get_variable_normal_range() (in module braviz.readAndFilter.tabular_data) get_variable_scenarios() (in module braviz.readAndFilter.user_data) get_variables() (ContextVariablesModel method) (ContextVariablesPanel method) (in module braviz.readAndFilter.tabular_data) get_window_level() (in module braviz.visualization.simple_vtk) getColorTransferLUT() (in module braviz.readAndFilter.surfer_input)

H

hide() (AdditionalCursors method) (SphereProp method) hide_checkpoints_bundle() (TractographyManager method) hide_cone() (SurfaceManager method)

hide_database_tract() (TractographyManager method) hide_image() (ImageManager method) (MeasurerViewer method) (OrthogonalPlanesViewer method) highlight() (AbstractPlot method)

I

image (fMRI_viewer attribute) (SubjectViewer attribute) image_plane_widget (ImageManager attribute) image_planes (MeasurerViewer attribute) (OrthogonalPlanesViewer attribute) ImageManager (class in braviz.visualization.subject_viewer) import_from_excel (module) import_or_error() (in module braviz.interaction.r_functions) IndexHandler (class in braviz.visualization.d3_visualizations) initialize() (OrientationAxes method) initialize_database() (in module braviz.readAndFilter.tabular_data) initialize_dynamic_data_dir() (BaseReader static method)

initialize_widget() (QCheckViewer method) (QFmriWidget method) (QMeasurerWidget method) (QOrthogonalPlanesWidget method) (QSubjectViewerWidget method) InteractionSelectDialog (class in braviz.interaction.qt_dialogs) InterceptPlot (class in braviz.visualization.matplotlib_qt_widget) is_leaf() (StructureTreeNode method) is_variable_name_nominal() (in module braviz.readAndFilter.tabular_data) is_variable_name_real() (in module braviz.readAndFilter.tabular_data) is_variable_nominal() (in module braviz.readAndFilter.tabular_data) is_variable_real() (in module braviz.readAndFilter.tabular_data) iter_id_list() (in module braviz.readAndFilter.filter_fibers)

K

Kmc400Reader (class in braviz.readAndFilter.kmc400)

Kmc40Reader (class in braviz.readAndFilter.kmc40)

L

LastUpdatedOrderedDict (class in braviz.readAndFilter.cache) LATERALITY (in module braviz.readAndFilter.tabular_data) LEFT_HANDED (in module braviz.readAndFilter.tabular_data) line_curvature() (in module braviz.readAndFilter.color_fibers) link_var_scenario() (in module braviz.readAndFilter.user_data) ListValidator (class in braviz.interaction.qt_widgets) load_from_cache() (BaseReader method) load_image() (AggregateInRoi method)

load_line() (in module braviz.readAndFilter.geom_db) load_sphere() (in module braviz.readAndFilter.geom_db) LoadLogicBundle (class in braviz.interaction.qt_dialogs) LoadScenarioDialog (class in braviz.interaction.qt_dialogs) LogicBundleNode (class in braviz.interaction.logic_bundle_model) LogicBundleNodeWithVTK (class in braviz.interaction.logic_bundle_model) LogicBundleQtTree (class in braviz.interaction.logic_bundle_model) LongPollMessageHandler (class in braviz.interaction.tornado_connection)

M

make_default_config() (in module braviz.readAndFilter.config_file) MatplotBarPlot (class in braviz.visualization.matplotlib_qt_widget) MatplotWidget (class in braviz.visualization.matplotlib_qt_widget) max_cache (CacheContainer attribute) mean_inside() (in module braviz.interaction.structure_metrics) MeasurerViewer (class in braviz.visualization.subject_viewer) memo_ten() (in module braviz.readAndFilter.cache) memoize() (in module braviz.readAndFilter.cache) MessageClient (class in braviz.interaction.connection)

MessageHandler (class in braviz.interaction.tornado_connection) MessagePlot (class in braviz.visualization.matplotlib_qt_widget) MessageServer (class in braviz.interaction.connection) ModelManager (class in braviz.visualization.subject_viewer) models (SubjectViewer attribute) move_img_from_subject() (BaseReader method) move_img_to_subject() (BaseReader method) MultiPlotOutcomeSelectDialog (class in braviz.interaction.qt_dialogs)

N

n_scans (SpmFileReader attribute) name (ConditionInfo attribute) (ContrastInfo attribute) NewVariableDialog (class in braviz.interaction.qt_dialogs) NewVariableValues (class in braviz.interaction.qt_models) nibNii2vtk() (in module braviz.readAndFilter.images)

nifti_rgb2vtk() (in module braviz.readAndFilter.images) node_type (LogicBundleNode attribute) NominalVariablesMeta (class in braviz.interaction.qt_models) numpy2vtk_img() (in module braviz.readAndFilter.images) numpy2vtkMatrix() (in module braviz.readAndFilter.transforms)

O

On() (persistentImagePlane method) onsets (ConditionInfo attribute) optimistic_reload_hierarchy() (StructureTreeModel method) OrientationAxes (class in braviz.visualization.simple_vtk)

orthogonal_viewer (QMeasurerWidget attribute) (QOrthogonalPlanesWidget attribute) OrthogonalPlanesViewer (class in braviz.visualization.subject_viewer) OutcomeSelectDialog (class in braviz.interaction.qt_dialogs) OutlineActor (class in braviz.visualization.simple_vtk)

P

ParallelCoordinatesHandler (class in braviz.visualization.d3_visualizations) parent (LogicBundleNode attribute) PassiveMessageClient (class in braviz.interaction.connection) pause (MessageServer attribute) persistentImagePlane (class in braviz.visualization.simple_vtk) pick_cone_actor (SurfaceManager attribute)

point1 (MeasurerViewer attribute) point2 (MeasurerViewer attribute) print_camera() (SubjectViewer method) PROJECT (in module braviz.readAndFilter) project_reader (class in braviz.readAndFilter) prop (LogicBundleNodeWithVTK attribute)

Q

QCheckViewer (class in braviz.visualization.checkerboard_view) QFmriWidget (class in braviz.visualization.subject_viewer) QMeasurerWidget (class in braviz.visualization.subject_viewer)

QOrthogonalPlanesWidget (class in braviz.visualization.subject_viewer) QSubjectViewerWidget (class in braviz.visualization.subject_viewer) qt_sample_select_dialog (module)

R

random_line() (in module braviz.readAndFilter.color_fibers) read_annot() (in module braviz.readAndFilter.surfer_input) read_free_surfer_csv_file() (in module braviz.readAndFilter.read_csv) read_logical_fibers() (in module braviz.readAndFilter.hierarchical_fibers) read_morph_data() (in module braviz.readAndFilter.surfer_input) read_surface() (in module braviz.readAndFilter.surfer_input) readFlirtMatrix() (in module braviz.readAndFilter.transforms) readFreeSurferTransform() (in module braviz.readAndFilter.transforms) receive_address (MessageServer attribute) recursive_delete_roi() (in module braviz.readAndFilter.geom_db) recursive_delete_subject() (in module braviz.readAndFilter.tabular_data) recursive_delete_variable() (in module braviz.readAndFilter.tabular_data) redraw() (AbstractPlot method) refresh_model() (BundlesSelectionList method) register_new_variable() (in module braviz.readAndFilter.tabular_data) RegressorSelectDialog (class in braviz.interaction.qt_dialogs) reload() (SamplesSelectionModel method)

reload_bundles() (TraculaManager method) reload_hierarchy() (StructureTreeModel method) reload_models() (ModelManager method) remove_filter() (SamplesFilterModel method) remove_from_renderer() (SphereProp method) remove_kid() (LogicBundleNode method) remove_nan_from_grid() (in module braviz.visualization.simple_vtk) remove_node() (LogicBundleQtTree method) reset_camera() (CheckboardView method) (MeasurerViewer method) (SubjectViewer method) (fMRI_viewer method) reset_data() (AnovaRegressorsModel method) reset_measure() (MeasurerViewer method) reset_window_level() (ImageManager method) ResidualsDiagnosticPlot (class in braviz.visualization.matplotlib_qt_widget) roi_name_exists() (in module braviz.readAndFilter.geom_db) root (LogicBundleQtTree attribute) RotatedLabel (class in braviz.interaction.qt_widgets)

S

sample_name_existst() (in module braviz.readAndFilter.user_data) SamplesFilterModel (class in braviz.interaction.qt_models) SamplesSelectionModel (class in braviz.interaction.qt_models) SampleTree (class in braviz.interaction.qt_models) save_checkpoints_bundle() (in module braviz.readAndFilter.bundles_db) save_into_cache() (BaseReader method) save_into_db() (NewVariableValues method) (NominalVariablesMeta method) save_is_real() (in module braviz.readAndFilter.tabular_data) save_is_real_by_name() (in module braviz.readAndFilter.tabular_data) save_line() (in module braviz.readAndFilter.geom_db) save_logic_bundle() (in module braviz.readAndFilter.bundles_db) save_nominal_labels() (in module braviz.readAndFilter.tabular_data) save_nominal_labels_by_name() (in module braviz.readAndFilter.tabular_data) save_real_meta() (in module braviz.readAndFilter.tabular_data) save_real_meta_by_name() (in module braviz.readAndFilter.tabular_data) save_ren_win_picture() (in module braviz.visualization.simple_vtk) save_scenario() (in module braviz.readAndFilter.user_data) save_sphere() (in module braviz.readAndFilter.geom_db) save_sub_sample() (in module braviz.readAndFilter.user_data) save_var_description() (in module braviz.readAndFilter.tabular_data) save_var_description_by_name() (in module braviz.readAndFilter.tabular_data) SaveFibersBundleDialog (class in braviz.interaction.qt_dialogs) SaveLogicFibersBundleDialog (class in braviz.interaction.qt_dialogs) SaveScenarioDialog (class in braviz.interaction.qt_dialogs) scalars_from_image() (in module braviz.readAndFilter.color_fibers) scalars_from_image_int() (in module braviz.readAndFilter.color_fibers) scalars_from_length() (in module braviz.readAndFilter.color_fibers) scalars_lines_from_image() (in module braviz.readAndFilter.color_fibers) ScatterPlot (class in braviz.visualization.matplotlib_qt_widget) ScenariosTableModel (class in braviz.interaction.qt_models) select_items() (VarListModel method) select_items_by_name() (VarListModel method) select_many_ids() (BundlesSelectionList method) SelectOneVariableWithFilter (class in braviz.interaction.qt_dialogs) send_json_message() (GenericMessageClient method) send_message() (GenericMessageClient method) (MessageClient method) (MessageServer method) (PassiveMessageClient method) server_broadcast (GenericMessageClient attribute) (MessageClient attribute) (PassiveMessageClient attribute) server_receive (GenericMessageClient attribute) (MessageClient attribute) (PassiveMessageClient attribute) set_active_db_tracts() (TractographyManager method) set_all() (fMRI_viewer method) set_axis_coords() (AdditionalCursors method) set_bundle() (FilterBundleWithSphere method) set_bundle_from_checkpoints() (TractographyManager method) set_bundles() (TraculaManager method) set_camera() (fMRI_viewer method) (MeasurerViewer method) (OrthogonalPlanesViewer method) (SubjectViewer method) set_center() (SphereProp method) set_checkeable() (NominalVariablesMeta method) set_color() (LogicBundleNodeWithVTK method) (ModelManager method) (RotatedLabel method) (SphereProp method) set_contour_opacity() (fMRI_viewer method) set_contour_value() (fMRI_viewer method) set_contour_visibility() (fMRI_viewer method) set_contours_visibility() (SubjectViewer method) set_current_space() (TractographyManager method) set_cursor() (cursors method) set_cursor_coords() (fMRI_viewer method) set_data_cols() (SubjectCheckTable method) set_delta() (cursors method) set_dimensions() (cursors method) set_elements() (SimpleSetModel method) set_fmri_contours_image() (SubjectViewer method) set_hemispheres() (SurfaceManager method) set_highlighted() (VarListModel method) set_ids() (SimpleBundlesList method) set_image() (AdditionalCursors method) (FmriContours method) set_image_level() (ImageManager method) set_image_slice() (CheckboardView method) (ImageManager method) set_image_window() (ImageManager method) set_images() (fMRI_blender method) set_img1() (CheckboardView method) set_img2() (CheckboardView method) set_input() (time_slice_viewer method)

set_input_data() (OutlineActor method) set_labels_dict() (NominalVariablesMeta method) set_list() (SubjectChecklist method) set_lut() (FmriContours method) set_luts() (fMRI_blender method) set_measure_axis() (MeasurerViewer method) set_measure_color() (MeasurerViewer method) set_models() (ModelManager method) set_number_of_divisions() (CheckboardView method) set_opacity() (LogicBundleNodeWithVTK method) (ModelManager method) (SphereProp method) (SurfaceManager method) (TractographyManager method) (TraculaManager method) set_orientation() (CheckboardView method) (persistentImagePlane method) set_origin() (cursors method) set_points() (MeasurerViewer method) set_radius() (SphereProp method) set_repr() (SphereProp method) set_root() (LogicBundleQtTree method) set_sample() (ContextVariablesPanel method) (SampleTree method) (SubjectsTable method) set_scalars() (SurfaceManager method) set_selected_structures() (StructureTreeModel method) set_selection() (SimpleCheckModel method) set_show_color_bar() (TractographyManager method) set_show_special() (SimpleBundlesList method) set_slice_coords() (MeasurerViewer method) set_space() (SurfaceManager method) set_spacing() (cursors method) set_subject() (ContextVariablesPanel method) (SurfaceManager method) (TractographyManager method) set_surface() (SurfaceManager method) set_time_point() (time_slice_viewer method) set_value() (FmriContours method) set_values_dict() (NewVariableValues method) set_var_columns() (SubjectsTable method) set_variables() (ContextVariablesPanel method) (SubjectDetails method) set_window_level() (time_slice_viewer method) set_z_spacing() (time_slice_viewer method) SetInputData() (OutlineActor method) (persistentImagePlane method) SetInteractor() (persistentImagePlane method) setLabelsLut() (persistentImagePlane method) show() (SphereProp method) show_color_bar() (SurfaceManager method) show_cone() (SubjectViewer method) show_image() (ImageManager method) (MeasurerViewer method) (OrthogonalPlanesViewer method) show_interactions() (AnovaRegressorsModel method) show_regressors() (AnovaRegressorsModel method) SimpleBundlesList (class in braviz.interaction.qt_models) SimpleCheckModel (class in braviz.interaction.qt_models) SimpleSetModel (class in braviz.interaction.qt_models) SimpleVtkViewer (class in braviz.visualization.simple_vtk) slice_change_handle() (QCheckViewer method) (QFmriWidget method) (QMeasurerWidget method) (QOrthogonalPlanesWidget method) (QSubjectViewerWidget method) solve_laterality() (in module braviz.interaction.structure_metrics) son_number (LogicBundleNode attribute) sphere (OrthogonalPlanesViewer attribute) SphereProp (class in braviz.visualization.subject_viewer) SpmFileReader (class in braviz.readAndFilter.read_spm) start() (SimpleVtkViewer method) start_server() (MessageServer method) stop() (GenericMessageClient method) (MessageClient method) (PassiveMessageClient method) stop_server() (MessageServer method) StructureTreeModel (class in braviz.interaction.qt_structures_model) StructureTreeNode (class in braviz.interaction.qt_structures_model) subject_viewer (QSubjectViewerWidget attribute) SubjectChecklist (class in braviz.interaction.qt_models) SubjectCheckTable (class in braviz.interaction.qt_models) SubjectDetails (class in braviz.interaction.qt_models) subjects_with_line() (in module braviz.readAndFilter.geom_db) subjects_with_sphere() (in module braviz.readAndFilter.geom_db) SubjectsTable (class in braviz.interaction.qt_models) SubjectViewer (class in braviz.visualization.subject_viewer) surface (SubjectViewer attribute) surface2vtkPolyData() (in module braviz.readAndFilter.surfer_input) SurfaceManager (class in braviz.visualization.subject_viewer) surfLUT2VTK() (in module braviz.readAndFilter.surfer_input)

T

text1_to_std() (persistentImagePlane method) text1_value_from_img() (persistentImagePlane method) time_slice_viewer (class in braviz.visualization.fmri_view) to_dict() (LogicBundleNode method) tr (SpmFileReader attribute) tractography (SubjectViewer attribute)

TractographyManager (class in braviz.visualization.subject_viewer) tracula (SubjectViewer attribute) TraculaManager (class in braviz.visualization.subject_viewer) transform_points_to_space() (BaseReader method) transformGeneralData() (in module braviz.readAndFilter.transforms) transformPolyData() (in module braviz.readAndFilter.transforms)

U

UBICAC (in module braviz.readAndFilter.tabular_data) update() (LogicBundleNodeWithVTK method) update_comment() (in module braviz.readAndFilter.user_data) update_guis() (in module braviz.interaction.generate_qt_guis) update_list() (VarAndGiniModel method) (VarListModel method) update_model() (NominalVariablesMeta method)

update_multiple_variable_values() (in module braviz.readAndFilter.tabular_data) update_pipeline() (CheckboardView method) update_scenario() (in module braviz.readAndFilter.user_data) update_variable_value() (in module braviz.readAndFilter.tabular_data) update_variable_values() (in module braviz.readAndFilter.tabular_data) update_view() (fMRI_viewer method)

V

VarAndGiniModel (class in braviz.interaction.qt_models) VariableSelectDialog (class in braviz.interaction.qt_dialogs) VarListModel (class in braviz.interaction.qt_models) verify_db_completeness() (in module braviz.readAndFilter.check_db)

viewer (QCheckViewer attribute) (QFmriWidget attribute) vtk2numpy() (in module braviz.readAndFilter.images) vtk_from_dict() (LogicBundleNodeWithVTK static method)

W

window_level_change_handle() (QFmriWidget method) (QMeasurerWidget method) (QOrthogonalPlanesWidget method) (QSubjectViewerWidget method) write_nib_image() (in module braviz.readAndFilter.images)

write_vtk_image() (in module braviz.readAndFilter.images)

X

x_image (MeasurerViewer attribute) (OrthogonalPlanesViewer attribute)

Y

y_image (MeasurerViewer attribute) (OrthogonalPlanesViewer attribute)

Z

z_image (MeasurerViewer attribute) (OrthogonalPlanesViewer attribute)