Index

A

activate_plugin() (brain_deer.presentation.qt.right_panel.RightPanel method) active() (brain_deer.warp.corrections.CorrectionSet method) active_filename() (in module brain_deer.presentation.qt.scene_3d_controls) add() (brain_deer.commands.registry.CommandRegistry method) add_base_mesh() (in module brain_deer.surface.plotting) add_layer_item() (brain_deer.presentation.qt.bottom_panel.LayerStackWidget method) add_measurement() (brain_deer.tools.roi_measurement.ROIManager method) add_new_layer() (brain_deer.presentation.qt.bottom_panel.LayerStackWidget method) add_observer() (brain_deer.commands.registry.CommandRegistry method) add_roi() (brain_deer.tools.roi_measurement.ROIManager method) add_scene_actor() (brain_deer.application.brain_deer_api.BrainDeerAPI method) add_tractogram_actor() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) add_view() (brain_deer.presentation.qt.perfect_layout.PerfectLayoutContainer method) add_view_overlay_item() (brain_deer.application.brain_deer_api.BrainDeerAPI method) advise_volume() (in module brain_deer.commands.advisor) affine (brain_deer.warp.field.DeformationField attribute) AgentRunner (class in brain_deer.plugins.braindeer_ai.agent) aggregate_inter_roi_depth_bins() (in module brain_deer.plugins.laminosaurus.analysis) all_positions() (brain_deer.surface.scene_model.SceneModel method) apply_bids_plugin_hooks() (in module brain_deer.infrastructure.bids.integrations)

apply_colormap_rgba() (in module brain_deer.presentation.colormap_registry) apply_corrections() (in module brain_deer.warp.apply) apply_display_resample_for_file() (in module brain_deer.presentation.qt.scene_3d_controls) apply_env_defaults() (brain_deer.app.cli.LaunchConfig method) apply_global_smoothing() (in module brain_deer.presentation.qt.scene_3d_controls) apply_material_to_targets() (in module brain_deer.presentation.qt.scene_3d_controls) apply_mesh_to_reference_space() (in module brain_deer.infrastructure.io.mesh) apply_opacity_for_file() (in module brain_deer.presentation.qt.scene_3d_controls) apply_preset() (in module brain_deer.surface.figures) apply_projection_target() (in module brain_deer.presentation.qt.bottom_panel) apply_spatial_smooth_for_file() (in module brain_deer.presentation.qt.scene_3d_controls) apply_streamline_settings() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) apply_streamline_visual_props_only() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) apply_subject_swap() (in module brain_deer.infrastructure.bids.swap) atlas_browser_2_widget() (in module brain_deer.presentation.qt.bottom_panel) atlas_browser_widget() (brain_deer.application.brain_deer_api.BrainDeerAPI method) atlas_row_structure_id() (in module brain_deer.presentation.qt.bottom_panel) auto_detect_atlas() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) auto_detect_template() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) available_colormaps() (brain_deer.application.brain_deer_api.BrainDeerAPI method) axis_codes() (in module brain_deer.infrastructure.orientation)

B

begin_interaction_capture() (brain_deer.application.brain_deer_api.BrainDeerAPI method) best_cloud_for_seed() (in module brain_deer.plugins.warpdrive.geometry) bids_action() (in module brain_deer.presentation.qt.bottom_panel) bids_layer_keys() (in module brain_deer.infrastructure.bids.session) BIDSDataset (class in brain_deer.infrastructure.bids.layout) bidsify_flat_folder() (in module brain_deer.infrastructure.bids.import_convert) BIDSItem (class in brain_deer.infrastructure.bids.entities) BIDSMapper (class in brain_deer.infrastructure.bids.mapper) BIDSMappingReviewDialog (class in brain_deer.presentation.qt.bids_mapping_dialog) BIDSPanel (class in brain_deer.presentation.qt.bids_panel) BIDSSessionState (class in brain_deer.infrastructure.bids.session) blender_widget() (brain_deer.application.brain_deer_api.BrainDeerAPI method) Brain3DView (class in brain_deer.presentation.qt.viewer_panel) brain_deer module brain_deer.app module brain_deer.app.cli module brain_deer.app.launch module brain_deer.app.startup module brain_deer.application module brain_deer.application.brain_deer_api module brain_deer.application.ports module brain_deer.application.ports.viewer module brain_deer.commands module brain_deer.commands.advisor module brain_deer.commands.analysis module brain_deer.commands.atlas_browser module brain_deer.commands.blender module brain_deer.commands.definitions module brain_deer.commands.leaddbs module brain_deer.commands.montage module brain_deer.commands.nl_intent module brain_deer.commands.preferences module brain_deer.commands.registry module brain_deer.commands.session module brain_deer.commands.warpdrive module brain_deer.domain module brain_deer.export module brain_deer.export.screenshot_export module brain_deer.infrastructure module brain_deer.infrastructure.bids module brain_deer.infrastructure.bids.datalad module brain_deer.infrastructure.bids.derivatives module brain_deer.infrastructure.bids.entities module brain_deer.infrastructure.bids.import_convert module brain_deer.infrastructure.bids.integrations module brain_deer.infrastructure.bids.layout module brain_deer.infrastructure.bids.loader module brain_deer.infrastructure.bids.mapper module brain_deer.infrastructure.bids.qc_batch module brain_deer.infrastructure.bids.rawimages module brain_deer.infrastructure.bids.session module brain_deer.infrastructure.bids.sidecar module brain_deer.infrastructure.bids.subject_switch module brain_deer.infrastructure.bids.swap module brain_deer.infrastructure.bids.tractometry module brain_deer.infrastructure.bids.validate module brain_deer.infrastructure.io module brain_deer.infrastructure.io.dicom module brain_deer.infrastructure.io.mesh module brain_deer.infrastructure.io.nifti module brain_deer.infrastructure.io.volume_proxy module brain_deer.infrastructure.orientation module brain_deer.plugin_api module brain_deer.plugin_api.v1 module brain_deer.plugins module brain_deer.plugins.braindeer_ai module brain_deer.plugins.braindeer_ai.agent module brain_deer.plugins.braindeer_ai.dev_context module brain_deer.plugins.braindeer_ai.plugin module brain_deer.plugins.braindeer_ai.prompts module brain_deer.plugins.braindeer_ai.scaffold module brain_deer.plugins.laminosaurus module brain_deer.plugins.laminosaurus.analysis module brain_deer.plugins.laminosaurus.plugin module brain_deer.plugins.laminosaurus.widget module brain_deer.plugins.leaddbs_atlas_widget module brain_deer.plugins.leaddbs_space_paths module brain_deer.plugins.leaddbs_stimulation_manager module brain_deer.plugins.leaddbs_stimulation_manager.plugin module brain_deer.plugins.leaddbs_stimulation_manager.widget module brain_deer.plugins.roi_studio module brain_deer.plugins.roi_studio.plugin module brain_deer.plugins.roi_studio.widget module

brain_deer.plugins.vr_stream module brain_deer.plugins.vr_stream.plugin module brain_deer.plugins.warpdrive module brain_deer.plugins.warpdrive.geometry module brain_deer.plugins.warpdrive.overlay2d module brain_deer.plugins.warpdrive.overlay3d module brain_deer.plugins.warpdrive.plugin module brain_deer.plugins.warpdrive.snap module brain_deer.plugins.warpdrive.style module brain_deer.plugins.warpdrive.tools module brain_deer.plugins.warpdrive.tools.base module brain_deer.plugins.warpdrive.tools.draw module brain_deer.plugins.warpdrive.tools.point_to_point module brain_deer.plugins.warpdrive.tools.shrink_expand module brain_deer.plugins.warpdrive.tools.smudge module brain_deer.plugins.warpdrive.widget module brain_deer.plugins_host module brain_deer.plugins_host.companion_registry module brain_deer.plugins_host.plugin_manager module brain_deer.presentation module brain_deer.presentation.colormap_registry module brain_deer.presentation.qt module brain_deer.presentation.qt.app_menu module brain_deer.presentation.qt.bids_import_dialog module brain_deer.presentation.qt.bids_mapping_dialog module brain_deer.presentation.qt.bids_panel module brain_deer.presentation.qt.bottom_panel module brain_deer.presentation.qt.colormap_editor module brain_deer.presentation.qt.command_palette module brain_deer.presentation.qt.invisible_splitter module brain_deer.presentation.qt.left_panel module brain_deer.presentation.qt.main_window module brain_deer.presentation.qt.panel_auto_hide_pin module brain_deer.presentation.qt.perfect_layout module brain_deer.presentation.qt.preferences_window module brain_deer.presentation.qt.projection_links module brain_deer.presentation.qt.right_panel module brain_deer.presentation.qt.scene_3d_controls module brain_deer.presentation.qt.scene_rig_controls module brain_deer.presentation.qt.sims_mode module brain_deer.presentation.qt.surface_studio_panel module brain_deer.presentation.qt.viewer_panel module brain_deer.presentation.typography module brain_deer.surface module brain_deer.surface.atlas module brain_deer.surface.connectome module brain_deer.surface.figures module brain_deer.surface.meshes module brain_deer.surface.plotting module brain_deer.surface.projection module brain_deer.surface.resources module brain_deer.surface.scene_model module brain_deer.surface.subcortical module brain_deer.surface.tracts module brain_deer.tools module brain_deer.tools.roi_measurement module brain_deer.utils module brain_deer.utils.fa_dec module brain_deer.utils.load_timing module brain_deer.warp module brain_deer.warp.apply module brain_deer.warp.corrections module brain_deer.warp.field module brain_deer.warp.io module brain_deer.warp.modifiable module brain_deer.warp.rbf module brain_deer.warp.session module braindeer_ai_system_prompt() (in module brain_deer.plugins.braindeer_ai.prompts) BrainDeerAPI (class in brain_deer.application.brain_deer_api) browse_atlas_directory() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) build_column_mask() (in module brain_deer.plugins.laminosaurus.analysis) build_connectome_scene() (in module brain_deer.surface.connectome) build_cortical_scene() (in module brain_deer.surface.plotting) build_default_registry() (in module brain_deer.commands) build_developer_pack() (in module brain_deer.plugins.braindeer_ai.dev_context) build_label_scene() (in module brain_deer.surface.plotting) build_rawimages() (in module brain_deer.infrastructure.bids.rawimages) build_startup_commands() (brain_deer.app.cli.LaunchConfig method) build_subcortical_scene() (in module brain_deer.surface.subcortical) build_tracts_scene() (in module brain_deer.surface.tracts) build_vertexwise_scene() (in module brain_deer.surface.plotting) build_voxelwise_scene() (in module brain_deer.surface.plotting) build_vtk_image_lut() (in module brain_deer.presentation.colormap_registry) build_vtk_lookup_table() (in module brain_deer.presentation.colormap_registry) bundled_plugins_dir() (in module brain_deer.plugins_host.plugin_manager)

C

cache_dir() (in module brain_deer.surface.resources) calculate_angle() (brain_deer.tools.roi_measurement.MeasurementCalculator static method) calculate_box_roi_stats() (brain_deer.tools.roi_measurement.ROIStatistics static method) calculate_distance() (brain_deer.tools.roi_measurement.MeasurementCalculator static method) calculate_polygon_area() (brain_deer.tools.roi_measurement.MeasurementCalculator static method) calculate_sphere_roi_stats() (brain_deer.tools.roi_measurement.ROIStatistics static method) camera_for_view() (in module brain_deer.surface.scene_model) CameraPose (class in brain_deer.surface.scene_model) candidate_template_paths() (in module brain_deer.plugins.leaddbs_space_paths) capture_screenshot() (brain_deer.application.brain_deer_api.BrainDeerAPI method) capture_widget() (brain_deer.export.screenshot_export.ScreenshotExporter static method) centroids_from_label_volume() (in module brain_deer.surface.connectome) change_streamline_set_color() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) choose_color() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) classify_dicom_series() (in module brain_deer.infrastructure.bids.import_convert) clear() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) clear_all() (brain_deer.tools.roi_measurement.ROIManager method) clear_all_plugins() (brain_deer.presentation.qt.right_panel.RightPanel method) clear_electrodes() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) clear_preview() (brain_deer.plugins.warpdrive.overlay2d.WarpOverlay2D method) clear_tractograms() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) close_plugin_tab() (brain_deer.presentation.qt.right_panel.RightPanel method) coarse_grid() (brain_deer.warp.session.WarpSession static method) coerce() (brain_deer.commands.registry.CommandParam method) CohortEntry (class in brain_deer.plugins.leaddbs_stimulation_manager.widget) ColorBarWidget (class in brain_deer.presentation.qt.colormap_editor) Coloring (class in brain_deer.surface.scene_model) ColormapGradientBar (class in brain_deer.presentation.qt.colormap_editor) ColumnColumnConnectivityResult (class in brain_deer.plugins.laminosaurus.analysis) combine_hemispheres() (in module brain_deer.surface.meshes) Command (class in brain_deer.commands.registry) CommandError CommandPalette (class in brain_deer.presentation.qt.command_palette) CommandParam (class in brain_deer.commands.registry) CommandRegistry (class in brain_deer.commands.registry) CommandResult (class in brain_deer.commands.registry) commit_dicom_import() (in module brain_deer.infrastructure.bids.import_convert) committed (brain_deer.plugins.warpdrive.tools.base.ToolResult attribute) complete_export() (in module brain_deer.presentation.qt.bottom_panel) compose() (in module brain_deer.warp.field) compose_grid() (in module brain_deer.surface.figures) compose_streaming() (in module brain_deer.warp.field) compose_streaming_outer() (in module brain_deer.warp.field)

compute_column_column_connectivity() (in module brain_deer.plugins.laminosaurus.analysis) compute_column_profiles() (in module brain_deer.plugins.laminosaurus.analysis) compute_column_summary() (in module brain_deer.plugins.laminosaurus.analysis) compute_control_metrics() (in module brain_deer.plugins.laminosaurus.analysis) compute_edges() (in module brain_deer.surface.connectome) compute_fa_dec() (in module brain_deer.utils.fa_dec) compute_inter_roi_layer_connectivity() (in module brain_deer.plugins.laminosaurus.analysis) compute_inter_roi_task_comparison() (in module brain_deer.plugins.laminosaurus.analysis) compute_laminar_seed_target_preference() (in module brain_deer.plugins.laminosaurus.analysis) compute_laminar_voxel_preference_map() (in module brain_deer.plugins.laminosaurus.analysis) compute_layer_connectivity() (in module brain_deer.plugins.laminosaurus.analysis) compute_layer_dynamics() (in module brain_deer.plugins.laminosaurus.analysis) compute_layer_profile() (in module brain_deer.plugins.laminosaurus.analysis) compute_orthogonal_sup_deep_cross_roi() (in module brain_deer.plugins.laminosaurus.analysis) compute_profile_comparison() (in module brain_deer.plugins.laminosaurus.analysis) compute_qc_dashboard() (in module brain_deer.plugins.laminosaurus.analysis) compute_seed_connectivity_map() (in module brain_deer.plugins.laminosaurus.analysis) configure_dbs_paths() (brain_deer.plugins.leaddbs_stimulation_manager.widget.StimulationManagerWidget method) ControlPoint (class in brain_deer.warp.corrections) CorrectionSet (class in brain_deer.warp.corrections) create_active_plugins_section() (brain_deer.presentation.qt.right_panel.RightPanel method) create_atlas_selection_section() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) create_available_plugins_section() (brain_deer.presentation.qt.right_panel.RightPanel method) create_bids_tab() (in module brain_deer.presentation.qt.bids_panel) (in module brain_deer.presentation.qt.bottom_panel) create_box_roi() (brain_deer.tools.roi_measurement.ROIMeasurementWidget method) create_composition_controls() (in module brain_deer.presentation.qt.bottom_panel) create_datalad_tab() (in module brain_deer.presentation.qt.bottom_panel) create_display_options_section() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) create_distance_measurement() (brain_deer.tools.roi_measurement.ROIMeasurementWidget method) create_electrode_section() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) create_export_tab() (in module brain_deer.presentation.qt.bottom_panel) create_global_composition_settings() (in module brain_deer.presentation.qt.bottom_panel) create_header() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) create_interactive_electrode() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) create_layer_composition_tab() (in module brain_deer.presentation.qt.bottom_panel) create_original_files_tab() (in module brain_deer.presentation.qt.bottom_panel) create_plugin_card() (brain_deer.presentation.qt.right_panel.RightPanel method) create_roi() (brain_deer.application.brain_deer_api.BrainDeerAPI method) create_sphere_roi() (brain_deer.tools.roi_measurement.ROIMeasurementWidget method) create_streamlines_section() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) create_structures_section() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) create_sweet_spots_section() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) CustomColormapDialog (class in brain_deer.presentation.qt.colormap_editor)

D

datalad_action() (in module brain_deer.presentation.qt.bottom_panel) deactivate_plugin() (brain_deer.presentation.qt.right_panel.RightPanel method) decompose_affine() (in module brain_deer.infrastructure.orientation) DeformationField (class in brain_deer.warp.field) depth_bin_index() (in module brain_deer.plugins.laminosaurus.analysis) derivative_summary() (in module brain_deer.infrastructure.bids.derivatives) DICOMLoader (class in brain_deer.infrastructure.io.dicom) DICOMSeries (class in brain_deer.infrastructure.io.dicom) discover_companion_addons() (in module brain_deer.plugins_host.companion_registry)

discover_dicom_subject_folders() (in module brain_deer.infrastructure.bids.import_convert) discover_labels_in_volume() (in module brain_deer.surface.subcortical) discover_patient_dirs() (in module brain_deer.plugins.leaddbs_stimulation_manager.widget) discover_plugins() (brain_deer.plugins_host.plugin_manager.PluginManager method) displacement (brain_deer.warp.field.DeformationField attribute) display_available_plugins() (brain_deer.presentation.qt.right_panel.RightPanel method) display_name_for_item() (in module brain_deer.infrastructure.bids.entities) display_to_image_coordinates() (brain_deer.application.brain_deer_api.BrainDeerAPI method) DrawTool (class in brain_deer.plugins.warpdrive.tools.draw) duplicate_layer() (brain_deer.presentation.qt.bottom_panel.LayerStackWidget method)

E

EdgesLayer (class in brain_deer.surface.scene_model) emit_event() (brain_deer.application.brain_deer_api.BrainDeerAPI method) ensure_uncompressed_nifti() (in module brain_deer.infrastructure.io.volume_proxy) evaluate_on_grid() (in module brain_deer.warp.rbf) evaluate_on_points() (in module brain_deer.warp.rbf) events_for_bold() (brain_deer.infrastructure.bids.layout.BIDSDataset method) example_plugin_card_clicked() (brain_deer.presentation.qt.right_panel.RightPanel method) expand_region_values_to_elements() (in module brain_deer.surface.atlas)

export_action() (in module brain_deer.presentation.qt.bottom_panel) export_combined_layers() (in module brain_deer.presentation.qt.bottom_panel) export_complete_scene() (in module brain_deer.presentation.qt.bottom_panel) export_individual_layers() (in module brain_deer.presentation.qt.bottom_panel) export_multiview_figure() (in module brain_deer.surface.figures) export_rotation_video() (in module brain_deer.surface.figures) export_scene_gltf() (in module brain_deer.surface.figures) export_to_file() (brain_deer.tools.roi_measurement.ROIManager method) extract_label_mesh() (in module brain_deer.surface.subcortical)

F

fallback_atlases_path_for_ui() (in module brain_deer.plugins.leaddbs_space_paths) fetch() (in module brain_deer.surface.resources)

filter_label_ids_from_info() (in module brain_deer.surface.subcortical) filter_plugins() (brain_deer.presentation.qt.right_panel.RightPanel method) find_tractometry_file() (in module brain_deer.infrastructure.bids.tractometry)

G

get_all_measurements() (brain_deer.tools.roi_measurement.ROIManager method) get_all_rois() (brain_deer.tools.roi_measurement.ROIManager method) get_atlas_regions() (in module brain_deer.surface.atlas) get_available_events() (brain_deer.application.brain_deer_api.BrainDeerAPI method) get_available_plugins() (brain_deer.plugins_host.plugin_manager.PluginManager method) get_available_resources() (in module brain_deer.surface.resources) get_button_stylesheet() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) get_checkbox_stylesheet() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) get_colormap_lut() (in module brain_deer.presentation.colormap_registry) get_combobox_stylesheet() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) get_corrected_crosshair() (brain_deer.application.brain_deer_api.BrainDeerAPI method) get_crosshair() (brain_deer.application.brain_deer_api.BrainDeerAPI method)

get_crosshair_world() (brain_deer.application.brain_deer_api.BrainDeerAPI method) get_current_data_info() (brain_deer.application.brain_deer_api.BrainDeerAPI method) get_data_at_position() (brain_deer.application.brain_deer_api.BrainDeerAPI method) get_groupbox_stylesheet() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) get_measurement() (brain_deer.tools.roi_measurement.ROIManager method) get_plugin_data_directory() (brain_deer.application.brain_deer_api.BrainDeerAPI method) get_plugin_metadata() (brain_deer.plugins_host.plugin_manager.PluginManager method) get_roi() (brain_deer.tools.roi_measurement.ROIManager method) get_slice_data() (brain_deer.application.brain_deer_api.BrainDeerAPI method) get_slider_stylesheet() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) get_stylesheet() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) guess_suffix_datatype() (in module brain_deer.infrastructure.bids.import_convert)

H

handle_3d_model_export() (in module brain_deer.presentation.qt.bottom_panel) handle_gltf_export() (in module brain_deer.presentation.qt.bottom_panel) handle_montage_export() (in module brain_deer.presentation.qt.bottom_panel) handle_multiview_export() (in module brain_deer.presentation.qt.bottom_panel) handle_screenshot_export() (in module brain_deer.presentation.qt.bottom_panel) handle_video_export() (in module brain_deer.presentation.qt.bottom_panel) handle_vtk_export() (in module brain_deer.presentation.qt.bottom_panel)

handle_web_export() (in module brain_deer.presentation.qt.bottom_panel) handle_x3d_export() (in module brain_deer.presentation.qt.bottom_panel) harden_corrections() (in module brain_deer.warp.apply) has_scene_inputs() (brain_deer.presentation.qt.surface_studio_panel.SurfaceStudioController method) hemi_for_view() (in module brain_deer.surface.scene_model) highlight_active_file() (in module brain_deer.presentation.qt.bottom_panel) huber_style_orthogonalized_sup_deep_composites() (in module brain_deer.plugins.laminosaurus.analysis) huber_style_orthogonalized_sup_deep_from_ts_matrix() (in module brain_deer.plugins.laminosaurus.analysis)

I

icon_path() (in module brain_deer.plugins.warpdrive.style) image_to_display_coordinates() (brain_deer.application.brain_deer_api.BrainDeerAPI method) import_bids_from_folder() (brain_deer.application.brain_deer_api.BrainDeerAPI method) import_dicom_folder() (in module brain_deer.presentation.qt.bottom_panel) import_dicom_to_bids() (in module brain_deer.infrastructure.bids.import_convert) import_from_file() (brain_deer.tools.roi_measurement.ROIManager method) ImportReviewRow (class in brain_deer.infrastructure.bids.import_convert) index_bids_layers_by_role() (in module brain_deer.infrastructure.bids.swap) infer_datatype() (in module brain_deer.infrastructure.bids.entities) initialize_plugin_system() (brain_deer.presentation.qt.right_panel.RightPanel method) install_app_menu() (in module brain_deer.presentation.qt.app_menu) install_panel_auto_hide_pin() (in module brain_deer.presentation.qt.panel_auto_hide_pin)

instantiate_plugin() (brain_deer.plugins_host.plugin_manager.PluginManager method) integrate_perfect_layout() (in module brain_deer.presentation.qt.perfect_layout) IntentRouter (class in brain_deer.commands.nl_intent) inter_roi_fc_split_half_block_reliability() (in module brain_deer.plugins.laminosaurus.analysis) inter_roi_layer_connectivity_from_timeseries() (in module brain_deer.plugins.laminosaurus.analysis) inter_roi_task_block_permutation_mean_abs_delta_r() (in module brain_deer.plugins.laminosaurus.analysis) interaction_capture_owner() (brain_deer.application.brain_deer_api.BrainDeerAPI method) InterRoiDepthBinSummary (class in brain_deer.plugins.laminosaurus.analysis) InterRoiLayerConnectivityResult (class in brain_deer.plugins.laminosaurus.analysis) InterRoiTaskComparisonResult (class in brain_deer.plugins.laminosaurus.analysis) invert() (in module brain_deer.warp.field) is_ras() (in module brain_deer.infrastructure.orientation) item_from_path() (in module brain_deer.infrastructure.bids.entities)

K

kwargs_shape() (brain_deer.commands.registry.Command method)

L

label_slice_contour() (in module brain_deer.plugins.warpdrive.geometry) LaminarSeedTargetResult (class in brain_deer.plugins.laminosaurus.analysis) LaminarVoxelPreferenceResult (class in brain_deer.plugins.laminosaurus.analysis) LaminosaurusWidget (class in brain_deer.plugins.laminosaurus.widget) LaunchConfig (class in brain_deer.app.cli) layer_correlation_matrix_from_timeseries() (in module brain_deer.plugins.laminosaurus.analysis) layer_hints_from_sidecar() (in module brain_deer.infrastructure.bids.sidecar) layer_overrides() (brain_deer.infrastructure.bids.mapper.BIDSMapper method) LayerStackItemWidget (class in brain_deer.presentation.qt.bottom_panel) LayerStackWidget (class in brain_deer.presentation.qt.bottom_panel) layerwise_mean_timeseries() (in module brain_deer.plugins.laminosaurus.analysis) layerwise_mean_timeseries_two_rois() (in module brain_deer.plugins.laminosaurus.analysis) leaddbs_reconstruction_mats() (in module brain_deer.infrastructure.bids.derivatives) leaddbs_space_root() (in module brain_deer.plugins.leaddbs_space_paths) leaddbs_subject_dir() (in module brain_deer.infrastructure.bids.derivatives) leaddbs_toolbox_root() (in module brain_deer.plugins.leaddbs_space_paths) LeadDBSAtlasWidget (class in brain_deer.plugins.leaddbs_atlas_widget) load_annot() (in module brain_deer.surface.atlas) load_bids_bundle() (brain_deer.application.brain_deer_api.BrainDeerAPI method) load_bids_items() (in module brain_deer.infrastructure.bids.loader) load_dbs_electrodes() (brain_deer.plugins.leaddbs_stimulation_manager.widget.StimulationManagerWidget method) load_example_plugins() (brain_deer.presentation.qt.right_panel.RightPanel method)

load_file() (brain_deer.application.brain_deer_api.BrainDeerAPI method) load_gifti_label() (in module brain_deer.surface.atlas) load_label_volume() (in module brain_deer.surface.atlas) load_mesh_electrode() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) load_mesh_for_3d() (in module brain_deer.infrastructure.io.mesh) load_nifti() (in module brain_deer.infrastructure.io.nifti) load_or_build_proxy() (in module brain_deer.infrastructure.io.volume_proxy) load_parcellation() (in module brain_deer.surface.atlas) load_registry_file() (in module brain_deer.surface.resources) load_streamline() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) load_streamline_as_isosurface() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) load_streamline_with_color() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) load_streamlines() (in module brain_deer.surface.tracts) load_structure_file() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) load_surface_geometry() (in module brain_deer.surface.meshes) load_sweet_spot() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) load_template() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) load_tractometry_scalars() (in module brain_deer.infrastructure.bids.tractometry) load_volume() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) local_intensity_snap() (in module brain_deer.plugins.warpdrive.snap) local_path() (in module brain_deer.surface.resources) logo_path() (in module brain_deer.plugins.warpdrive.style) lps_to_ras_points() (in module brain_deer.warp.io)

M

MacroRecorder (class in brain_deer.commands.session) MacroStore (class in brain_deer.commands.session) map_data_to_regions() (in module brain_deer.surface.atlas) map_source (brain_deer.plugins.warpdrive.tools.base.ToolContext attribute) mask_from_column_labels() (in module brain_deer.plugins.laminosaurus.analysis) mask_nifti_to_label_ids() (in module brain_deer.surface.subcortical) match_path_counts() (in module brain_deer.plugins.warpdrive.geometry) maybe_load_fullres_into_ram() (in module brain_deer.infrastructure.io.volume_proxy) Measurement (class in brain_deer.tools.roi_measurement) MeasurementCalculator (class in brain_deer.tools.roi_measurement) MeasurementType (class in brain_deer.tools.roi_measurement) methods_text() (brain_deer.commands.session.SessionJournal method) module brain_deer brain_deer.app brain_deer.app.cli brain_deer.app.launch brain_deer.app.startup brain_deer.application brain_deer.application.brain_deer_api brain_deer.application.ports brain_deer.application.ports.viewer brain_deer.commands brain_deer.commands.advisor brain_deer.commands.analysis brain_deer.commands.atlas_browser brain_deer.commands.blender brain_deer.commands.definitions brain_deer.commands.leaddbs brain_deer.commands.montage brain_deer.commands.nl_intent brain_deer.commands.preferences brain_deer.commands.registry brain_deer.commands.session brain_deer.commands.warpdrive brain_deer.domain brain_deer.export brain_deer.export.screenshot_export brain_deer.infrastructure brain_deer.infrastructure.bids brain_deer.infrastructure.bids.datalad brain_deer.infrastructure.bids.derivatives brain_deer.infrastructure.bids.entities brain_deer.infrastructure.bids.import_convert brain_deer.infrastructure.bids.integrations brain_deer.infrastructure.bids.layout brain_deer.infrastructure.bids.loader brain_deer.infrastructure.bids.mapper brain_deer.infrastructure.bids.qc_batch brain_deer.infrastructure.bids.rawimages brain_deer.infrastructure.bids.session brain_deer.infrastructure.bids.sidecar brain_deer.infrastructure.bids.subject_switch brain_deer.infrastructure.bids.swap brain_deer.infrastructure.bids.tractometry brain_deer.infrastructure.bids.validate brain_deer.infrastructure.io brain_deer.infrastructure.io.dicom brain_deer.infrastructure.io.mesh brain_deer.infrastructure.io.nifti brain_deer.infrastructure.io.volume_proxy brain_deer.infrastructure.orientation brain_deer.plugin_api brain_deer.plugin_api.v1 brain_deer.plugins brain_deer.plugins.braindeer_ai brain_deer.plugins.braindeer_ai.agent brain_deer.plugins.braindeer_ai.dev_context brain_deer.plugins.braindeer_ai.plugin brain_deer.plugins.braindeer_ai.prompts brain_deer.plugins.braindeer_ai.scaffold brain_deer.plugins.laminosaurus brain_deer.plugins.laminosaurus.analysis brain_deer.plugins.laminosaurus.plugin brain_deer.plugins.laminosaurus.widget brain_deer.plugins.leaddbs_atlas_widget brain_deer.plugins.leaddbs_space_paths brain_deer.plugins.leaddbs_stimulation_manager brain_deer.plugins.leaddbs_stimulation_manager.plugin brain_deer.plugins.leaddbs_stimulation_manager.widget brain_deer.plugins.roi_studio brain_deer.plugins.roi_studio.plugin brain_deer.plugins.roi_studio.widget brain_deer.plugins.vr_stream brain_deer.plugins.vr_stream.plugin brain_deer.plugins.warpdrive brain_deer.plugins.warpdrive.geometry brain_deer.plugins.warpdrive.overlay2d brain_deer.plugins.warpdrive.overlay3d brain_deer.plugins.warpdrive.plugin brain_deer.plugins.warpdrive.snap brain_deer.plugins.warpdrive.style brain_deer.plugins.warpdrive.tools brain_deer.plugins.warpdrive.tools.base brain_deer.plugins.warpdrive.tools.draw brain_deer.plugins.warpdrive.tools.point_to_point brain_deer.plugins.warpdrive.tools.shrink_expand brain_deer.plugins.warpdrive.tools.smudge brain_deer.plugins.warpdrive.widget brain_deer.plugins_host brain_deer.plugins_host.companion_registry brain_deer.plugins_host.plugin_manager brain_deer.presentation brain_deer.presentation.colormap_registry brain_deer.presentation.qt brain_deer.presentation.qt.app_menu brain_deer.presentation.qt.bids_import_dialog brain_deer.presentation.qt.bids_mapping_dialog brain_deer.presentation.qt.bids_panel brain_deer.presentation.qt.bottom_panel brain_deer.presentation.qt.colormap_editor brain_deer.presentation.qt.command_palette brain_deer.presentation.qt.invisible_splitter brain_deer.presentation.qt.left_panel brain_deer.presentation.qt.main_window brain_deer.presentation.qt.panel_auto_hide_pin brain_deer.presentation.qt.perfect_layout brain_deer.presentation.qt.preferences_window brain_deer.presentation.qt.projection_links brain_deer.presentation.qt.right_panel brain_deer.presentation.qt.scene_3d_controls brain_deer.presentation.qt.scene_rig_controls brain_deer.presentation.qt.sims_mode brain_deer.presentation.qt.surface_studio_panel brain_deer.presentation.qt.viewer_panel brain_deer.presentation.typography brain_deer.surface brain_deer.surface.atlas brain_deer.surface.connectome brain_deer.surface.figures brain_deer.surface.meshes brain_deer.surface.plotting brain_deer.surface.projection brain_deer.surface.resources brain_deer.surface.scene_model brain_deer.surface.subcortical brain_deer.surface.tracts brain_deer.tools brain_deer.tools.roi_measurement brain_deer.utils brain_deer.utils.fa_dec brain_deer.utils.load_timing brain_deer.warp brain_deer.warp.apply brain_deer.warp.corrections brain_deer.warp.field brain_deer.warp.io brain_deer.warp.modifiable brain_deer.warp.rbf brain_deer.warp.session

mono_font() (in module brain_deer.presentation.typography) mono_font_family() (in module brain_deer.presentation.typography) mutual_orthogonalize_timeseries() (in module brain_deer.plugins.laminosaurus.analysis)

N

names_to_label_ids() (in module brain_deer.surface.subcortical) nearest_points_on_cloud() (in module brain_deer.plugins.warpdrive.geometry)

needs_display_proxy() (in module brain_deer.infrastructure.io.volume_proxy) needs_fullres_cache() (in module brain_deer.infrastructure.io.volume_proxy)

O

on_disease_changed() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) on_hemisphere_changed() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) on_layer_reordered() (brain_deer.presentation.qt.bottom_panel.LayerStackWidget method) on_max_streamlines_changed() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) on_opacity_changed() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) (brain_deer.presentation.qt.bottom_panel.LayerStackItemWidget method) on_streamline_filter_changed() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) on_tube_radius_changed() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method)

on_visibility_changed() (brain_deer.presentation.qt.bottom_panel.LayerStackItemWidget method) open_bids_dataset() (brain_deer.application.brain_deer_api.BrainDeerAPI method) open_dataset() (in module brain_deer.infrastructure.bids.layout) open_dataset_path() (brain_deer.presentation.qt.bids_panel.BIDSPanel method) open_pie_for_2d() (brain_deer.presentation.qt.sims_mode.SimsModeController method) open_screenshot_export() (in module brain_deer.presentation.qt.bottom_panel) OrthogonalSupDeepCrossRoiResult (class in brain_deer.plugins.laminosaurus.analysis) owns_3d_layer() (brain_deer.presentation.qt.surface_studio_panel.SurfaceStudioController method)

P

Parcellation (class in brain_deer.surface.atlas) parse_bids_filename() (in module brain_deer.infrastructure.bids.entities) parse_launch_args() (in module brain_deer.app.cli) parse_threshold() (in module brain_deer.surface.projection) pending_source (brain_deer.plugins.warpdrive.tools.base.ToolResult attribute) pending_target (brain_deer.plugins.warpdrive.tools.base.ToolResult attribute) PerfectLayoutContainer (class in brain_deer.presentation.qt.perfect_layout) pick_streamline_color() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) plan_dicom_import() (in module brain_deer.infrastructure.bids.import_convert) plan_subject_swap() (in module brain_deer.infrastructure.bids.swap) plane_basis() (in module brain_deer.plugins.warpdrive.geometry) Plugin (class in brain_deer.plugins.braindeer_ai.plugin) (class in brain_deer.plugins.laminosaurus.plugin) (class in brain_deer.plugins.leaddbs_stimulation_manager.plugin) (class in brain_deer.plugins.roi_studio.plugin) (class in brain_deer.plugins.vr_stream.plugin) (class in brain_deer.plugins.warpdrive.plugin)

plugin_card_clicked() (brain_deer.presentation.qt.right_panel.RightPanel method) PluginManager (class in brain_deer.plugins_host.plugin_manager) PointsLayer (class in brain_deer.surface.scene_model) PointToPointTool (class in brain_deer.plugins.warpdrive.tools.point_to_point) populate_vtk_color_transfer_function() (in module brain_deer.presentation.colormap_registry) popup_centered() (brain_deer.presentation.qt.sims_mode.SimsPieMenu method) prepare_array_for_3d() (in module brain_deer.infrastructure.io.volume_proxy) project_vol2streamlines() (in module brain_deer.surface.projection) project_vol2surf() (in module brain_deer.surface.projection) projection_pairs() (brain_deer.infrastructure.bids.mapper.BIDSMapper method) projection_target_candidates() (in module brain_deer.presentation.qt.bottom_panel) projection_targets_of() (in module brain_deer.presentation.qt.projection_links) proxy_affine() (in module brain_deer.infrastructure.io.volume_proxy)

Q

qss_mono_family() (in module brain_deer.presentation.typography)

qss_ui_family() (in module brain_deer.presentation.typography)

R

rawimages_path_for() (in module brain_deer.infrastructure.bids.rawimages) read_correction_set() (in module brain_deer.warp.io) read_displacement_field() (in module brain_deer.warp.io) read_region_data() (in module brain_deer.surface.atlas) reapply_atlas_tract_projections() (in module brain_deer.presentation.qt.bottom_panel) rebuild_glyphs() (brain_deer.plugins.warpdrive.overlay2d.WarpOverlay2D method) reference_grid_for_resample() (in module brain_deer.infrastructure.io.nifti) refresh_file_row_3d_ui() (in module brain_deer.presentation.qt.bottom_panel) refresh_surface_row_targets() (in module brain_deer.presentation.qt.bottom_panel) region_rgb_to_elements() (in module brain_deer.surface.atlas) register_analysis_commands() (in module brain_deer.commands.analysis) register_interaction_handler() (brain_deer.application.brain_deer_api.BrainDeerAPI method) register_resource() (in module brain_deer.surface.resources) register_session_commands() (in module brain_deer.commands.session) register_viewer_commands() (in module brain_deer.commands.definitions) release_plugin() (brain_deer.plugins_host.plugin_manager.PluginManager method) remove() (brain_deer.warp.corrections.CorrectionSet method) remove_file() (brain_deer.application.brain_deer_api.BrainDeerAPI method) remove_layer_item() (brain_deer.presentation.qt.bottom_panel.LayerStackWidget method) remove_measurement() (brain_deer.tools.roi_measurement.ROIManager method) remove_roi() (brain_deer.tools.roi_measurement.ROIManager method) remove_selected_file() (in module brain_deer.presentation.qt.bottom_panel) remove_selected_layer() (brain_deer.presentation.qt.bottom_panel.LayerStackWidget method) remove_streamline_set() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) reorder_files() (in module brain_deer.presentation.qt.bottom_panel) reorient_to_ras() (in module brain_deer.infrastructure.io.nifti)

replace_layer_payload() (in module brain_deer.infrastructure.bids.swap) replace_stack_widget_at() (brain_deer.presentation.qt.right_panel.ScrollingPluginTabs method) resample_field() (in module brain_deer.warp.field) resample_path() (in module brain_deer.plugins.warpdrive.geometry) resample_to_reference() (in module brain_deer.infrastructure.io.nifti) resample_to_reference_with_stride() (in module brain_deer.infrastructure.io.nifti) reset() (brain_deer.plugins.warpdrive.tools.base.WarpTool method) reset_camera_3d() (brain_deer.application.brain_deer_api.BrainDeerAPI method) resizeEvent() (brain_deer.presentation.qt.perfect_layout.PerfectLayoutContainer method) resolve_mesh_reference() (in module brain_deer.infrastructure.io.mesh) Resource (class in brain_deer.surface.resources) ResourceUnavailableError review_mapping() (in module brain_deer.presentation.qt.bids_mapping_dialog) RightPanel (class in brain_deer.presentation.qt.right_panel) ROI (class in brain_deer.tools.roi_measurement) ROIManager (class in brain_deer.tools.roi_measurement) ROIMeasurementWidget (class in brain_deer.tools.roi_measurement) ROIStatistics (class in brain_deer.tools.roi_measurement) ROIType (class in brain_deer.tools.roi_measurement) role_key_for_entities() (in module brain_deer.infrastructure.bids.entities) role_key_for_item() (in module brain_deer.infrastructure.bids.entities) role_key_from_bids_meta() (in module brain_deer.infrastructure.bids.entities) rotate_camera_3d() (brain_deer.application.brain_deer_api.BrainDeerAPI method) run_bids_bundle_all_subjects() (brain_deer.application.brain_deer_api.BrainDeerAPI method) run_bids_validator() (in module brain_deer.infrastructure.bids.validate) run_bundle_all_subjects() (in module brain_deer.infrastructure.bids.qc_batch)

S

sample() (brain_deer.warp.field.DeformationField method) save() (brain_deer.infrastructure.bids.mapper.BIDSMapper method) save_image() (brain_deer.export.screenshot_export.ScreenshotExporter static method) scalar_slice_to_rgba() (in module brain_deer.presentation.colormap_registry) scalar_values_to_rgba() (in module brain_deer.presentation.colormap_registry) scene_to_preset() (in module brain_deer.surface.figures) SceneModel (class in brain_deer.surface.scene_model) schedule() (brain_deer.app.startup.StartupRunner method) ScreenshotExporter (class in brain_deer.export.screenshot_export) ScreenshotExportWidget (class in brain_deer.export.screenshot_export) ScrollingPluginTabs (class in brain_deer.presentation.qt.right_panel) search() (brain_deer.commands.registry.CommandRegistry method) select_labels() (in module brain_deer.surface.subcortical) SessionJournal (class in brain_deer.commands.session) set_3d_crosshair_color() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) set_atlas_path() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) set_background_color_3d() (brain_deer.application.brain_deer_api.BrainDeerAPI method) set_brain_model_opacity() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) set_brain_model_threshold() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) set_brain_model_visible() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) set_camera_view_3d() (brain_deer.application.brain_deer_api.BrainDeerAPI method) set_crosshair() (brain_deer.application.brain_deer_api.BrainDeerAPI method) set_file_visibility() (brain_deer.application.brain_deer_api.BrainDeerAPI method) set_layout() (brain_deer.application.brain_deer_api.BrainDeerAPI method) set_layout_mode() (brain_deer.presentation.qt.perfect_layout.PerfectLayoutContainer method) set_orientation() (brain_deer.application.brain_deer_api.BrainDeerAPI method) set_projection_targets() (in module brain_deer.presentation.qt.projection_links) set_selected_file() (brain_deer.application.brain_deer_api.BrainDeerAPI method) set_streamline_point_colors() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) set_toolbar() (brain_deer.presentation.qt.perfect_layout.PerfectLayoutContainer method) set_tractogram_visibility() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) setup_ui() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) show_error_message() (brain_deer.presentation.qt.right_panel.RightPanel method) show_no_plugins_message() (brain_deer.presentation.qt.right_panel.RightPanel method) show_notification() (brain_deer.application.brain_deer_api.BrainDeerAPI method) show_plugin() (brain_deer.presentation.qt.right_panel.RightPanel method) show_slice() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) showEvent() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) shrink_expand_ring() (in module brain_deer.plugins.warpdrive.geometry) ShrinkExpandTool (class in brain_deer.plugins.warpdrive.tools.shrink_expand) SimsModeController (class in brain_deer.presentation.qt.sims_mode)

SimsPieMenu (class in brain_deer.presentation.qt.sims_mode) SimsTarget (class in brain_deer.presentation.qt.sims_mode) slice_mask() (in module brain_deer.plugins.laminosaurus.analysis) SmudgeTool (class in brain_deer.plugins.warpdrive.tools.smudge) snapshot_target_geometry() (brain_deer.presentation.qt.surface_studio_panel.SurfaceStudioController method) solve() (brain_deer.warp.session.WarpSession method) solve_weights() (in module brain_deer.warp.rbf) spacing (brain_deer.warp.field.DeformationField property) split_bids_extension() (in module brain_deer.infrastructure.bids.entities) split_layer_labels_superficial_deep() (in module brain_deer.plugins.laminosaurus.analysis) start_streaming() (brain_deer.plugins.vr_stream.plugin.Plugin method) StartupCommand (class in brain_deer.app.cli) StartupRunner (class in brain_deer.app.startup) StickyComboBox (class in brain_deer.presentation.qt.bottom_panel) stimulation_manager_widget() (brain_deer.application.brain_deer_api.BrainDeerAPI method) StimulationManagerWidget (class in brain_deer.plugins.leaddbs_stimulation_manager.widget) stop_streaming() (brain_deer.plugins.vr_stream.plugin.Plugin method) streamline_points_for_set() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) streamline_scalars_to_rgba() (in module brain_deer.surface.projection) style_panel_auto_hide_pin() (in module brain_deer.presentation.qt.panel_auto_hide_pin) subsample() (in module brain_deer.surface.tracts) subscribe_to_event() (brain_deer.application.brain_deer_api.BrainDeerAPI method) suggest_proxy_stride() (in module brain_deer.infrastructure.io.volume_proxy) surface_export_figure() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_get_atlas_regions() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_list_resources() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_open() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_plot_connectome() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_plot_cortical() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_plot_subcortical() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_plot_tracts() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_plot_vertexwise() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_plot_voxelwise() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_project_vol2surf() (brain_deer.application.brain_deer_api.BrainDeerAPI method) surface_set_view() (brain_deer.application.brain_deer_api.BrainDeerAPI method) SurfaceGeometry (class in brain_deer.surface.meshes) SurfaceLayer (class in brain_deer.surface.scene_model) SurfaceStudioController (class in brain_deer.presentation.qt.surface_studio_panel) switch_bids_subject() (brain_deer.application.brain_deer_api.BrainDeerAPI method) (in module brain_deer.infrastructure.bids.subject_switch) sync_projections_from_layers() (brain_deer.infrastructure.bids.mapper.BIDSMapper method)

T

take_measurement() (brain_deer.application.brain_deer_api.BrainDeerAPI method) target_filenames() (in module brain_deer.presentation.qt.scene_3d_controls) timed_load() (in module brain_deer.utils.load_timing) to_dict() (brain_deer.tools.roi_measurement.Measurement method) (brain_deer.tools.roi_measurement.ROI method) to_ras() (in module brain_deer.infrastructure.orientation) to_vtk_polydata() (in module brain_deer.surface.meshes) toggle_3d_crosshair_visibility() (brain_deer.presentation.qt.viewer_panel.Brain3DView method)

toggle_available_section() (brain_deer.presentation.qt.right_panel.RightPanel method) toggle_interactive_manipulation() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) toggle_streamline_set_visibility() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) toggle_structure() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) ToolContext (class in brain_deer.plugins.warpdrive.tools.base) ToolResult (class in brain_deer.plugins.warpdrive.tools.base) TractLayer (class in brain_deer.surface.scene_model) transform_points() (brain_deer.warp.field.DeformationField method) TwoDViewerPort (class in brain_deer.application.ports.viewer)

U

ui_font() (in module brain_deer.presentation.typography) ui_font_family() (in module brain_deer.presentation.typography) undo_to_source_frame() (brain_deer.warp.session.WarpSession method) unload_bids_layers() (in module brain_deer.infrastructure.bids.subject_switch) unsubscribe_from_event() (brain_deer.application.brain_deer_api.BrainDeerAPI method) update() (brain_deer.warp.corrections.CorrectionSet method)

update_crosshair_position() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) update_plugin_counter() (brain_deer.presentation.qt.right_panel.RightPanel method) update_preview() (brain_deer.plugins.warpdrive.overlay2d.WarpOverlay2D method) update_remove_button_state() (in module brain_deer.presentation.qt.bottom_panel) update_rendering() (brain_deer.presentation.qt.viewer_panel.Brain3DView method) update_stack_info() (brain_deer.presentation.qt.bottom_panel.LayerStackWidget method) update_stl_transform() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method)

V

validate_dataset() (in module brain_deer.infrastructure.bids.layout) viewer_capabilities_catalog() (in module brain_deer.plugins.braindeer_ai.prompts) visualize_example_electrode() (brain_deer.plugins.leaddbs_atlas_widget.LeadDBSAtlasWidget method) volume_block_lists_from_bids_events() (in module brain_deer.plugins.laminosaurus.analysis) volume_indices_from_bids_events() (in module brain_deer.plugins.laminosaurus.analysis)

VolumeDataSinkPort (class in brain_deer.application.ports.viewer) voxel_to_world() (in module brain_deer.infrastructure.orientation) voxelwise_threshold() (in module brain_deer.surface.projection) voxelwise_threshold_multi() (in module brain_deer.surface.projection) VRStreamControlWidget (class in brain_deer.plugins.vr_stream.plugin)

W

warp_existing_targets() (in module brain_deer.warp.modifiable) warp_slice() (brain_deer.plugins.warpdrive.overlay2d.WarpOverlay2D static method) WarpApplyError warpdrive_widget() (brain_deer.application.brain_deer_api.BrainDeerAPI method) WarpOverlay2D (class in brain_deer.plugins.warpdrive.overlay2d) WarpOverlay3D (class in brain_deer.plugins.warpdrive.overlay3d) WarpSession (class in brain_deer.warp.session)

WarpTool (class in brain_deer.plugins.warpdrive.tools.base) with_all_hardened() (brain_deer.warp.corrections.CorrectionSet method) within_roi_layer_correlation_matrix() (in module brain_deer.plugins.laminosaurus.analysis) world_to_voxel() (in module brain_deer.infrastructure.orientation) write_correction_set() (in module brain_deer.warp.io) write_displacement_field() (in module brain_deer.warp.io) write_rawimages_for_subject() (in module brain_deer.infrastructure.bids.rawimages)

Z

zoom() (brain_deer.application.brain_deer_api.BrainDeerAPI method)