Index _ | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W _ _atlas_fetchers_mne (coord2region.AtlasFetcher attribute) (coord2region.fetching.AtlasFetcher attribute) _atlas_fetchers_nilearn (coord2region.AtlasFetcher attribute) (coord2region.fetching.AtlasFetcher attribute) _coords_fetchers_nilearn (coord2region.AtlasFetcher attribute) (coord2region.fetching.AtlasFetcher attribute) A add_watermark() (in module coord2region.utils) (in module coord2region.utils.image_utils) AIModelInterface (class in coord2region) (class in coord2region.ai_model_interface) allowed_domains (coord2region.ai_reports.ReasonedReportContext attribute) (coord2region.ReasonedReportContext attribute) anthropic_api_key (coord2region.config.Coord2RegionConfig attribute) atlas (coord2region.ai_reports.ReasonedReportContext attribute) (coord2region.ReasonedReportContext attribute) Atlas Fetcher Atlas Mapper atlas_configs (coord2region.config.Coord2RegionConfig attribute) atlas_names (coord2region.config.Coord2RegionConfig attribute) atlas_notes (coord2region.ai_reports.ReasonedReportContext attribute) (coord2region.ReasonedReportContext attribute) ATLAS_URLS (coord2region.AtlasFetcher attribute) (coord2region.fetching.AtlasFetcher attribute) AtlasFetcher (class in coord2region) (class in coord2region.fetching) AtlasFileHandler (class in coord2region) (class in coord2region.utils) (class in coord2region.utils.file_handler) AtlasMapper (class in coord2region) (class in coord2region.coord2region) B batch_mni_to_region_index() (coord2region.BatchAtlasMapper method) (coord2region.coord2region.BatchAtlasMapper method) batch_mni_to_region_name() (coord2region.BatchAtlasMapper method) (coord2region.coord2region.BatchAtlasMapper method) batch_mni_to_region_names() (coord2region.coord2region.MultiAtlasMapper method) (coord2region.MultiAtlasMapper method) batch_mni_to_voxel() (coord2region.BatchAtlasMapper method) (coord2region.coord2region.BatchAtlasMapper method) batch_region_index_from_name() (coord2region.BatchAtlasMapper method) (coord2region.coord2region.BatchAtlasMapper method) batch_region_index_to_mni() (coord2region.BatchAtlasMapper method) (coord2region.coord2region.BatchAtlasMapper method) batch_region_name_from_index() (coord2region.BatchAtlasMapper method) (coord2region.coord2region.BatchAtlasMapper method) batch_region_name_to_mni() (coord2region.BatchAtlasMapper method) (coord2region.coord2region.BatchAtlasMapper method) (coord2region.coord2region.MultiAtlasMapper method) (coord2region.MultiAtlasMapper method) batch_size (coord2region.config.Coord2RegionConfig attribute) batch_voxel_to_mni() (coord2region.BatchAtlasMapper method) (coord2region.coord2region.BatchAtlasMapper method) BatchAtlasMapper (class in coord2region) (class in coord2region.coord2region) boundary_proximity_mm (coord2region.ai_reports.ReasonedReportContext attribute) (coord2region.ReasonedReportContext attribute) build_generation_summary() (in module coord2region.ai_model_interface) build_interface() (in module coord2region.ai_helpers) build_pipeline_config() (coord2region.config.Coord2RegionConfig method) build_reasoned_report_messages() (in module coord2region) (in module coord2region.ai_reports) build_region_image_request() (in module coord2region) (in module coord2region.ai_reports) build_side_by_side_panel() (in module coord2region.utils.image_utils) Builder C cached_data_dir (coord2region.AtlasFileHandler attribute), [1] (coord2region.utils.AtlasFileHandler attribute), [1] (coord2region.utils.file_handler.AtlasFileHandler attribute), [1] collect_inputs() (coord2region.config.Coord2RegionConfig method) command line option coords-to-atlas coords-to-image coords-to-insights coords-to-study coords-to-summary region-to-coords region-to-insights region-to-study region-to-summary run Config File convert_system() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) convert_to_mni() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) convert_to_source() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) coord2region module coord2region.ai_helpers module coord2region.ai_model_interface module coord2region.ai_reports module coord2region.cli module coord2region.config module coord2region.coord2region module coord2region.coord2study module coord2region.fetching module coord2region.llm module coord2region.paths module coord2region.pipeline module coord2region.utils module coord2region.utils.file_handler module coord2region.utils.image_utils module coord2region.utils.paths module coord2region.utils.utils module Coord2RegionConfig (class in coord2region.config) coordinate (coord2region.pipeline.PipelineResult attribute) coordinate_mni (coord2region.ai_reports.ReasonedReportContext attribute) (coord2region.ReasonedReportContext attribute) coordinates (coord2region.config.Coord2RegionConfig attribute) coordinates_file (coord2region.config.Coord2RegionConfig attribute) coords-to-atlas command line option coords-to-image command line option coords-to-insights command line option coords-to-study command line option coords-to-summary command line option create_parser() (in module coord2region.cli) custom_prompt (coord2region.config.Coord2RegionConfig attribute) D data_dir (coord2region.AtlasFetcher attribute), [1] (coord2region.AtlasFileHandler attribute), [1] (coord2region.fetching.AtlasFetcher attribute), [1] (coord2region.utils.AtlasFileHandler attribute), [1] (coord2region.utils.file_handler.AtlasFileHandler attribute), [1] deduplicate_datasets() (in module coord2region) (in module coord2region.coord2study) DEFAULT_NEGATIVE_PROMPT (in module coord2region) (in module coord2region.ai_reports) DEFAULT_SYSTEM_MESSAGE (in module coord2region) (in module coord2region.ai_reports) distance_to_region_boundary() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) distance_to_region_centroid() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) E email_for_abstracts (coord2region.config.Coord2RegionConfig attribute) ensure_mne_data_directory() (in module coord2region.utils) (in module coord2region.utils.paths) F fetch_atlas() (coord2region.AtlasFetcher method) (coord2region.fetching.AtlasFetcher method) fetch_datasets() (in module coord2region) (in module coord2region.coord2study) fetch_from_local() (coord2region.AtlasFileHandler method) (coord2region.utils.AtlasFileHandler method) (coord2region.utils.file_handler.AtlasFileHandler method) fetch_from_url() (coord2region.AtlasFileHandler method) (coord2region.utils.AtlasFileHandler method) (coord2region.utils.file_handler.AtlasFileHandler method) fetch_labels() (in module coord2region.utils) (in module coord2region.utils.utils) file_handler (coord2region.AtlasFetcher attribute), [1] (coord2region.fetching.AtlasFetcher attribute), [1] format_instructions (coord2region.ai_reports.ReasonedReportContext attribute) (coord2region.ReasonedReportContext attribute) G gemini_api_key (coord2region.config.Coord2RegionConfig attribute) generate_batch_summaries() (in module coord2region) (in module coord2region.llm) generate_image() (coord2region.ai_model_interface.AIModelInterface method) (coord2region.AIModelInterface method) generate_llm_prompt() (in module coord2region) (in module coord2region.llm) generate_mni152_image() (in module coord2region) (in module coord2region.llm) (in module coord2region.utils) (in module coord2region.utils.image_utils) generate_region_image() (in module coord2region) (in module coord2region.llm) generate_region_image_prompt() (in module coord2region.llm) generate_summary() (in module coord2region) (in module coord2region.llm) generate_summary_async() (in module coord2region) (in module coord2region.llm) generate_text() (coord2region.ai_model_interface.AIModelInterface method) (coord2region.ai_model_interface.ModelProvider method) (coord2region.AIModelInterface method) generate_text_async() (coord2region.ai_model_interface.AIModelInterface method) (coord2region.ai_model_interface.ModelProvider method) (coord2region.AIModelInterface method) generated_images_dir (coord2region.AtlasFileHandler attribute), [1] (coord2region.utils.AtlasFileHandler attribute), [1] (coord2region.utils.file_handler.AtlasFileHandler attribute), [1] get_studies_for_coordinate() (in module coord2region) (in module coord2region.coord2study) get_working_directory() (in module coord2region) (in module coord2region.paths) getenv_str() (in module coord2region.ai_helpers) H HCP_LICENSE_ENV (in module coord2region.fetching) HCP_LICENSE_PATH (in module coord2region.fetching) hdr (coord2region.AtlasMapper attribute) (coord2region.coord2region.AtlasMapper attribute) hemisphere (coord2region.ai_reports.ReasonedReportContext attribute) (coord2region.ReasonedReportContext attribute) huggingface_api_key (coord2region.config.Coord2RegionConfig attribute) huggingface_credentials_present() (in module coord2region.ai_model_interface) I image (coord2region.pipeline.PipelineResult attribute) image_backend (coord2region.config.Coord2RegionConfig attribute) image_custom_prompt (coord2region.config.Coord2RegionConfig attribute) image_model (coord2region.config.Coord2RegionConfig attribute) IMAGE_MODEL_CANDIDATES (in module coord2region.ai_helpers) IMAGE_PROMPT_TEMPLATES (in module coord2region) (in module coord2region.llm) image_prompt_type (coord2region.config.Coord2RegionConfig attribute) images (coord2region.pipeline.PipelineResult attribute) indexes (coord2region.AtlasMapper attribute), [1] (coord2region.coord2region.AtlasMapper attribute), [1] infer_hemisphere() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) (in module coord2region) (in module coord2region.ai_reports) input_type (coord2region.config.Coord2RegionConfig attribute) inputs (coord2region.config.Coord2RegionConfig attribute) J json_data (coord2region.ai_reports.ReasonedReport attribute) (coord2region.ReasonedReport attribute) json_error (coord2region.ai_reports.ReasonedReport attribute) (coord2region.ReasonedReport attribute) json_text (coord2region.ai_reports.ReasonedReport attribute) (coord2region.ReasonedReport attribute) L labels (coord2region.AtlasMapper attribute), [1] (coord2region.coord2region.AtlasMapper attribute), [1] legacy_config (coord2region.config.Coord2RegionConfig attribute) list_all_regions() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) list_available_atlases() (coord2region.AtlasFetcher method) (coord2region.fetching.AtlasFetcher method) list_available_models() (coord2region.ai_model_interface.AIModelInterface method) (coord2region.AIModelInterface method) LLM_PROMPT_TEMPLATES (in module coord2region) (in module coord2region.llm) load() (coord2region.AtlasFileHandler method) (coord2region.AtlasMapper class method) (coord2region.coord2region.AtlasMapper class method) (coord2region.coord2region.MultiAtlasMapper class method) (coord2region.MultiAtlasMapper class method) (coord2region.utils.AtlasFileHandler method) (coord2region.utils.file_handler.AtlasFileHandler method) load_deduplicated_dataset() (in module coord2region) (in module coord2region.coord2study) load_env_file() (in module coord2region.ai_model_interface) load_environment() (in module coord2region.ai_helpers) logger (in module coord2region.coord2region) (in module coord2region.coord2study) (in module coord2region.fetching) (in module coord2region.utils.file_handler) M main() (in module coord2region.cli) mapper (coord2region.BatchAtlasMapper attribute), [1] (coord2region.coord2region.BatchAtlasMapper attribute), [1] mappers (coord2region.coord2region.MultiAtlasMapper attribute), [1] (coord2region.MultiAtlasMapper attribute), [1] max_atlases (coord2region.config.Coord2RegionConfig attribute) membership_scores() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) mne_data_dir (coord2region.AtlasFileHandler attribute), [1] (coord2region.utils.AtlasFileHandler attribute), [1] (coord2region.utils.file_handler.AtlasFileHandler attribute), [1] MNI152 mni_coordinates (coord2region.pipeline.PipelineResult attribute) mni_to_region_index() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) mni_to_region_name() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) mni_to_vertex() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) mni_to_voxel() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) model_config (coord2region.config.Coord2RegionConfig attribute) ModelProvider (class in coord2region.ai_model_interface) models (coord2region.ai_model_interface.ModelProvider attribute) module coord2region coord2region.ai_helpers coord2region.ai_model_interface coord2region.ai_reports coord2region.cli coord2region.config coord2region.coord2region coord2region.coord2study coord2region.fetching coord2region.llm coord2region.paths coord2region.pipeline coord2region.utils coord2region.utils.file_handler coord2region.utils.image_utils coord2region.utils.paths coord2region.utils.utils MultiAtlasMapper (class in coord2region) (class in coord2region.coord2region) N name (coord2region.AtlasMapper attribute), [1] (coord2region.coord2region.AtlasMapper attribute), [1] narrative (coord2region.ai_reports.ReasonedReport attribute) (coord2region.ReasonedReport attribute) nilearn_data (coord2region.AtlasFetcher attribute), [1] (coord2region.AtlasFileHandler attribute), [1] (coord2region.fetching.AtlasFetcher attribute), [1] (coord2region.utils.AtlasFileHandler attribute), [1] (coord2region.utils.file_handler.AtlasFileHandler attribute), [1] NiMARE O openai_api_key (coord2region.config.Coord2RegionConfig attribute) openrouter_api_key (coord2region.config.Coord2RegionConfig attribute) output_format (coord2region.config.Coord2RegionConfig attribute) output_name (coord2region.config.Coord2RegionConfig attribute) outputs (coord2region.config.Coord2RegionConfig attribute) P pack_surf_output() (in module coord2region.utils) (in module coord2region.utils.utils) pack_vol_output() (in module coord2region.utils) (in module coord2region.utils.utils) parse_reasoned_report_output() (in module coord2region) (in module coord2region.ai_reports) PathLike (in module coord2region.utils.paths) pick_first_supported_model() (in module coord2region.ai_model_interface) Pipeline PipelineResult (class in coord2region.pipeline) prepare_datasets() (in module coord2region) (in module coord2region.coord2study) prompt_type (coord2region.config.Coord2RegionConfig attribute) PromptType (in module coord2region.ai_model_interface) Provider provider_name() (coord2region.ai_model_interface.AIModelInterface method) (coord2region.AIModelInterface method) providers (coord2region.config.Coord2RegionConfig attribute) R ReasonedReport (class in coord2region) (class in coord2region.ai_reports) ReasonedReportContext (class in coord2region) (class in coord2region.ai_reports) Recipe region-to-coords command line option region-to-insights command line option region-to-study command line option region-to-summary command line option region_centroid() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) region_index_from_name() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) region_index_to_mni() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) region_labels (coord2region.pipeline.PipelineResult attribute) region_name_from_index() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) region_name_to_mni() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) region_names (coord2region.config.Coord2RegionConfig attribute) region_search_radius (coord2region.config.Coord2RegionConfig attribute) regions (coord2region.AtlasMapper attribute) (coord2region.coord2region.AtlasMapper attribute) register_provider() (coord2region.ai_model_interface.AIModelInterface method) (coord2region.AIModelInterface method) remove_duplicate_studies() (in module coord2region.coord2study) resolve_working_directory() (in module coord2region.utils) (in module coord2region.utils.paths) Result Directory results_dir (coord2region.AtlasFileHandler attribute), [1] (coord2region.utils.AtlasFileHandler attribute), [1] (coord2region.utils.file_handler.AtlasFileHandler attribute), [1] run command line option run_from_config() (in module coord2region.cli) run_pipeline() (in module coord2region) (in module coord2region.pipeline) run_reasoned_report() (in module coord2region) (in module coord2region.ai_reports) S save() (coord2region.AtlasFileHandler method) (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) (coord2region.coord2region.MultiAtlasMapper method) (coord2region.MultiAtlasMapper method) (coord2region.utils.AtlasFileHandler method) (coord2region.utils.file_handler.AtlasFileHandler method) save_as_csv() (in module coord2region.utils) (in module coord2region.utils.file_handler) save_as_pdf() (in module coord2region.utils) (in module coord2region.utils.file_handler) save_batch_folder() (in module coord2region.utils) (in module coord2region.utils.file_handler) search_studies() (in module coord2region) (in module coord2region.coord2study) select_model() (in module coord2region.ai_helpers) shape (coord2region.AtlasMapper attribute) (coord2region.coord2region.AtlasMapper attribute) sources (coord2region.config.Coord2RegionConfig attribute) stream_generate_text() (coord2region.ai_model_interface.AIModelInterface method) (coord2region.ai_model_interface.ModelProvider method) (coord2region.AIModelInterface method) stream_summary() (in module coord2region) (in module coord2region.llm) studies (coord2region.ai_reports.ReasonedReportContext attribute) (coord2region.pipeline.PipelineResult attribute) (coord2region.ReasonedReportContext attribute) Study Radius study_search_radius (coord2region.config.Coord2RegionConfig attribute) subjects_dir (coord2region.AtlasFetcher attribute), [1] (coord2region.AtlasFileHandler attribute), [1] (coord2region.fetching.AtlasFetcher attribute), [1] (coord2region.utils.AtlasFileHandler attribute), [1] (coord2region.utils.file_handler.AtlasFileHandler attribute), [1] summaries (coord2region.pipeline.PipelineResult attribute) summary (coord2region.pipeline.PipelineResult attribute) summary_max_tokens (coord2region.config.Coord2RegionConfig attribute) summary_models (coord2region.config.Coord2RegionConfig attribute) supports() (coord2region.ai_model_interface.AIModelInterface method) (coord2region.ai_model_interface.ModelProvider method) (coord2region.AIModelInterface method) supports_batching (coord2region.ai_model_interface.ModelProvider attribute) supports_batching() (coord2region.ai_model_interface.AIModelInterface method) (coord2region.AIModelInterface method) system (coord2region.AtlasMapper attribute), [1] (coord2region.coord2region.AtlasMapper attribute), [1] T TEXT_MODEL_CANDIDATES (in module coord2region.ai_helpers) to_pipeline_runtime() (coord2region.config.Coord2RegionConfig method) U use_cached_dataset (coord2region.config.Coord2RegionConfig attribute) V vertex_to_mni() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) vertex_to_region (coord2region.AtlasMapper attribute) (coord2region.coord2region.AtlasMapper attribute) vol (coord2region.AtlasMapper attribute) (coord2region.coord2region.AtlasMapper attribute) voxel_to_mni() (coord2region.AtlasMapper method) (coord2region.coord2region.AtlasMapper method) W warnings (coord2region.pipeline.PipelineResult attribute) Web Runner working_directory (coord2region.config.Coord2RegionConfig attribute)
