Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | P | R | S | T | U | V A add_bind_path() (nipoppy.config.container.ContainerConfig method) (nipoppy.config.ContainerConfig method) add_bind_path_to_args() (in module nipoppy.config.container) add_logfile() (in module nipoppy.logger) add_or_update_records() (nipoppy.tabular.base.BaseTabular method) add_path_suffix() (in module nipoppy.utils) add_path_timestamp() (in module nipoppy.utils) add_pybids_ignore_patterns() (in module nipoppy.utils) ALL_CNR_COLS (in module script) ANALYSIS_LEVEL (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) API apply_analysis_level() (in module nipoppy.workflows.pipeline) apply_fname_mapping() (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) apply_substitutions_to_json() (in module nipoppy.utils) (nipoppy.config.Config method) (nipoppy.config.main.Config method) APPTAINER_BIND_FLAG (in module nipoppy.config.container) APPTAINER_BIND_SEP (in module nipoppy.config.container) APPTAINER_ENVVAR_PREFIXES (in module nipoppy.config.container) ARGS (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) B bagel (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) BIDS bids_participant_id (nipoppy.tabular.bagel.BagelModel attribute) BIDS_PIPELINES (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) bids_session_id (nipoppy.tabular.bagel.BagelModel attribute) BIDS_SESSION_PREFIX (in module nipoppy.env) bids_source (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) BIDS_SUBJECT_PREFIX (in module nipoppy.env) Boutiques boutiques_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) BOUTIQUES_CONFIG_KEY (in module nipoppy.config.boutiques) BOUTIQUES_CUSTOM_KEY (in module nipoppy.config.boutiques) build_parser() (in module script) C capture_warnings() (in module nipoppy.logger) check_container_args() (in module nipoppy.config.container) check_container_command() (in module nipoppy.config.container) check_dicoms (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) check_dir() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_input() (nipoppy.config.Config class method) (nipoppy.config.main.Config class method) check_participant_id() (in module nipoppy.utils) check_pipeline_step() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_pipeline_version() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) check_session_id() (in module nipoppy.utils) check_status() (nipoppy.tabular.bagel.BagelModel class method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.tracker.PipelineTracker method) CLI col_bids_participant_id (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_bids_session_id (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_datatype (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) col_in_bids (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) col_in_post_reorg (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) col_in_pre_reorg (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) col_participant_dicom_dir (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) col_participant_id (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) col_pipeline (nipoppy.workflows.dataset_status.StatusWorkflow attribute) col_pipeline_name (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_pipeline_step (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_pipeline_version (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_session_id (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) col_status (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) col_visit_id (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) COMMAND (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) concatenate() (nipoppy.tabular.base.BaseTabular method) conda config (nipoppy.layout.DatasetLayout attribute) (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) CONTAINER_CONFIG CONTAINER_INFO (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) CONTAINER_SUBCOMMAND (nipoppy.config.boutiques.BoutiquesConfig attribute) (nipoppy.config.BoutiquesConfig attribute) copy() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) copy_files (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) copytree() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) create_bids_db() (in module nipoppy.utils) create_symlink() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) CUSTOM (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) D DATASET_NAME (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) datatype (nipoppy.tabular.manifest.ManifestModel attribute) DATE_FORMAT (in module nipoppy.logger) DEFAULT_CNR_COLS (in module script) DEFAULT_CNR_VOL_PATHS (in module script) DEFAULT_EULER_SURF_PATHS (in module script) DEFAULT_LAYOUT_INFO (in module nipoppy.layout) DEFAULT_MODE (in module script) DEFAULT_PIPELINE_STEP_NAME (in module nipoppy.env) DEFAULT_SES_COLNAME (in module script) DEFAULT_SES_PREFIX (in module script) DEFAULT_SUB_COLNAME (in module script) DEFAULT_SUB_PREFIX (in module script) DESCRIPTION (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) description (nipoppy.layout.PathInfo attribute) descriptor (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) DESCRIPTOR_FILE (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) dicom_dir_map (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) DICOM_DIR_MAP_FILE (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) DICOM_DIR_PARTICIPANT_FIRST (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) dname_pipeline_idp (nipoppy.layout.DatasetLayout attribute) dname_pipeline_output (nipoppy.layout.DatasetLayout attribute) doughnut (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) Doughnut file dpath_assessments (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_bids (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_code (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_containers (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_DATA (in module nipoppy.utils) dpath_derivatives (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_descriptions (nipoppy.layout.DatasetLayout property) dpath_downloads (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) DPATH_EXAMPLES (in module nipoppy.utils) DPATH_LAYOUTS (in module nipoppy.utils) dpath_logs (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_pipeline (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_bids_db (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_idp (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) dpath_pipeline_output (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipeline_work (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) dpath_pipelines (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_post_reorg (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_pre_reorg (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_pybids_db (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_root (nipoppy.layout.DatasetLayout attribute) (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) DPATH_SAMPLE_PIPELINES (in module nipoppy.utils) dpath_scratch (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_sourcedata (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_src_imaging (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_src_tabular (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_tabular (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpath_work (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) dpaths (nipoppy.layout.DatasetLayout property) dpaths_to_check (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) (nipoppy.workflows.PipelineRunner property) (nipoppy.workflows.runner.PipelineRunner property) dry_run (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) E empty (nipoppy.workflows.doughnut.DoughnutWorkflow attribute) (nipoppy.workflows.DoughnutWorkflow attribute) ENV_VARS (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) equals() (nipoppy.tabular.base.BaseTabular method) EXTRACTION_PIPELINES (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) F FAILURE (nipoppy.env.LogColor attribute) FAKE_SESSION_ID (in module nipoppy.env) FIELD_DESCRIPTION_MAP (in module nipoppy.utils) FILE (nipoppy.config.container.ContainerInfo attribute) find_duplicates() (nipoppy.tabular.base.BaseTabular method) fname_readme (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) FORMAT_FILE (in module nipoppy.logger) FORMAT_RICH (in module nipoppy.logger) fpath_config (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_container (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) FPATH_DEFAULT_LAYOUT (in module nipoppy.utils) fpath_demographics (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_doughnut (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_imaging_bagel (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) fpath_layout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) fpath_manifest (nipoppy.layout.DatasetLayout attribute) (nipoppy.layout.LayoutConfig attribute) FPATH_SAMPLE_CONFIG (in module nipoppy.utils) FPATH_SAMPLE_CONFIG_FULL (in module nipoppy.utils) FPATH_SAMPLE_DICOM_DIR_MAP (in module nipoppy.utils) FPATH_SAMPLE_MANIFEST (in module nipoppy.utils) fpath_spec (nipoppy.layout.DatasetLayout attribute) fpaths (nipoppy.layout.DatasetLayout property) G generate_doughnut() (in module nipoppy.tabular) (in module nipoppy.tabular.doughnut) generate_fpath_log() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) GENERATE_PYBIDS_DATABASE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) get_bidsified_participants_sessions() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) get_boutiques_config_from_descriptor() (in module nipoppy.config.boutiques) get_completed_participants_sessions() (nipoppy.tabular.Bagel method) (nipoppy.tabular.bagel.Bagel method) get_dicom_dir() (nipoppy.tabular.dicom_dir_map.DicomDirMap method) get_diff() (nipoppy.tabular.base.BaseTabular method) get_downloaded_participants_sessions() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) get_dpath_pipeline() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_idp() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_output() (nipoppy.layout.DatasetLayout method) get_dpath_pipeline_work() (nipoppy.layout.DatasetLayout method) get_dpath_pybids_db() (nipoppy.layout.DatasetLayout method) get_fpath_container() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig method) get_fpaths_to_reorg() (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) get_full_path() (nipoppy.layout.DatasetLayout method) get_imaging_subset() (nipoppy.tabular.Manifest method) (nipoppy.tabular.manifest.Manifest method) get_logger() (in module nipoppy.logger) get_organized_participants_sessions() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) get_participants_sessions() (nipoppy.tabular.Manifest method) (nipoppy.tabular.manifest.Manifest method) get_participants_sessions_to_run() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.ExtractionRunner method) (nipoppy.workflows.extractor.ExtractionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) get_path_info() (nipoppy.layout.LayoutConfig method) get_paths() (nipoppy.layout.DatasetLayout method) get_pipeline_config() (in module nipoppy.config.main) get_pipeline_tag() (in module nipoppy.utils) get_pipeline_version() (in module nipoppy.config.main) get_series_class() (nipoppy.tabular.base.BaseTabular method) get_status() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) get_step_config() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig method) group (nipoppy.config.pipeline_step.AnalysisLevelType attribute) H HPC I Imaging bagel file in_bids (nipoppy.tabular.doughnut.DoughnutModel attribute) in_post_reorg (nipoppy.tabular.doughnut.DoughnutModel attribute) in_pre_reorg (nipoppy.tabular.doughnut.DoughnutModel attribute) index_cols (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) (nipoppy.tabular.base.BaseTabular attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) INHERIT (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.ContainerConfig attribute) invocation (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) INVOCATION_FILE (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) is_derived_dicom() (in module nipoppy.workflows.dicom_reorg) IS_TESTING (in module nipoppy.env) J JSON K keep_workdir (nipoppy.workflows.PipelineRunner attribute) (nipoppy.workflows.runner.PipelineRunner attribute) L launch_boutiques_run() (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.runner.PipelineRunner method) layout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) load() (nipoppy.config.Config class method) (nipoppy.config.main.Config class method) (nipoppy.tabular.base.BaseTabular class method) (nipoppy.tabular.Manifest class method) (nipoppy.tabular.manifest.Manifest class method) load_json() (in module nipoppy.utils) load_or_generate() (nipoppy.tabular.dicom_dir_map.DicomDirMap class method) log_command() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) log_prefix_run (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) log_prefix_run_stderr (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) log_prefix_run_stdout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) LOG_SUFFIX (in module nipoppy.workflows.base) logger (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) M manifest (nipoppy.workflows.base.BaseWorkflow property) (nipoppy.workflows.BaseWorkflow property) merge() (nipoppy.config.container.ContainerConfig method) (nipoppy.config.ContainerConfig method) mkdir() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) MODE_MULTI (in module script) MODE_SINGLE (in module script) model (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) (nipoppy.tabular.base.BaseTabular property) (nipoppy.tabular.dicom_dir_map.DicomDirMap attribute) (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) model_config (nipoppy.config.BidsPipelineConfig attribute) (nipoppy.config.BidsPipelineStepConfig attribute) (nipoppy.config.boutiques.BoutiquesConfig attribute) (nipoppy.config.BoutiquesConfig attribute) (nipoppy.config.Config attribute) (nipoppy.config.container.ContainerConfig attribute) (nipoppy.config.container.ContainerInfo attribute) (nipoppy.config.ContainerConfig attribute) (nipoppy.config.main.Config attribute) (nipoppy.config.pipeline.BidsPipelineConfig attribute) (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) (nipoppy.config.pipeline.PipelineInfo attribute) (nipoppy.config.pipeline.ProcPipelineConfig attribute) (nipoppy.config.pipeline_step.BidsPipelineStepConfig attribute) (nipoppy.config.pipeline_step.ExtractionPipelineStepConfig attribute) (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) (nipoppy.config.tracker.TrackerConfig attribute) (nipoppy.config.TrackerConfig attribute) (nipoppy.layout.LayoutConfig attribute) (nipoppy.tabular.manifest.ManifestModel attribute) module nipoppy nipoppy.base nipoppy.config nipoppy.config.boutiques nipoppy.config.container nipoppy.config.main nipoppy.config.pipeline nipoppy.config.pipeline_step nipoppy.config.tracker nipoppy.env nipoppy.layout nipoppy.logger nipoppy.tabular nipoppy.tabular.bagel nipoppy.tabular.base nipoppy.tabular.dicom_dir_map nipoppy.tabular.doughnut nipoppy.tabular.manifest nipoppy.utils nipoppy.workflows nipoppy.workflows.base nipoppy.workflows.bids_conversion nipoppy.workflows.dataset_init nipoppy.workflows.dataset_status nipoppy.workflows.dicom_reorg nipoppy.workflows.doughnut nipoppy.workflows.extractor nipoppy.workflows.pipeline nipoppy.workflows.runner nipoppy.workflows.tracker script MRI N n_success (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) n_total (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow attribute) (nipoppy.workflows.DicomReorgWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) NAME (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.BasePipelineStepConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline.PipelineInfo attribute) (nipoppy.config.pipeline_step.BasePipelineStepConfig attribute) name (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) (nipoppy.workflows.bids_conversion.BidsConversionRunner attribute) (nipoppy.workflows.BidsConversionRunner attribute) (nipoppy.workflows.ExtractionRunner attribute) (nipoppy.workflows.extractor.ExtractionRunner attribute) nipoppy module nipoppy.base module nipoppy.base.Base (built-in class) nipoppy.config module nipoppy.config.BasePipelineConfig (built-in class) nipoppy.config.BasePipelineStepConfig (built-in class) nipoppy.config.BidsPipelineConfig (built-in class) nipoppy.config.BidsPipelineStepConfig (built-in class) nipoppy.config.boutiques module nipoppy.config.boutiques.BoutiquesConfig (built-in class) nipoppy.config.BoutiquesConfig (built-in class) nipoppy.config.Config (built-in class) nipoppy.config.container module nipoppy.config.container.ContainerConfig (built-in class) nipoppy.config.container.ContainerInfo (built-in class) nipoppy.config.ContainerConfig (built-in class) nipoppy.config.main module nipoppy.config.main.Config (built-in class) nipoppy.config.pipeline module nipoppy.config.pipeline.BasePipelineConfig (built-in class) nipoppy.config.pipeline.BidsPipelineConfig (built-in class) nipoppy.config.pipeline.ExtractionPipelineConfig (built-in class) nipoppy.config.pipeline.PipelineInfo (built-in class) nipoppy.config.pipeline.ProcPipelineConfig (built-in class) nipoppy.config.pipeline_step module nipoppy.config.pipeline_step.AnalysisLevelType (built-in class) nipoppy.config.pipeline_step.BasePipelineStepConfig (built-in class) nipoppy.config.pipeline_step.BidsPipelineStepConfig (built-in class) nipoppy.config.pipeline_step.ExtractionPipelineStepConfig (built-in class) nipoppy.config.pipeline_step.ProcPipelineStepConfig (built-in class) nipoppy.config.ProcPipelineConfig (built-in class) nipoppy.config.ProcPipelineStepConfig (built-in class) nipoppy.config.tracker module nipoppy.config.tracker.TrackerConfig (built-in class) nipoppy.config.TrackerConfig (built-in class) nipoppy.env module nipoppy.env.LogColor (built-in class) nipoppy.env.ReturnCode (built-in class) nipoppy.layout module nipoppy.layout.DatasetLayout (built-in class) nipoppy.layout.DpathInfo (built-in class) nipoppy.layout.FpathInfo (built-in class) nipoppy.layout.LayoutConfig (built-in class) nipoppy.layout.OptionalFpathInfo (built-in class) nipoppy.layout.PathInfo (built-in class) nipoppy.logger module nipoppy.tabular module nipoppy.tabular.bagel module nipoppy.tabular.Bagel (built-in class) nipoppy.tabular.bagel.Bagel (built-in class) nipoppy.tabular.bagel.BagelModel (built-in class) nipoppy.tabular.base module nipoppy.tabular.base.BaseTabular (built-in class) nipoppy.tabular.base.BaseTabularModel (built-in class) nipoppy.tabular.dicom_dir_map module nipoppy.tabular.dicom_dir_map.DicomDirMap (built-in class) nipoppy.tabular.dicom_dir_map.DicomDirMapModel (built-in class) nipoppy.tabular.doughnut module nipoppy.tabular.Doughnut (built-in class) nipoppy.tabular.doughnut.Doughnut (built-in class) nipoppy.tabular.doughnut.DoughnutModel (built-in class) nipoppy.tabular.manifest module nipoppy.tabular.Manifest (built-in class) nipoppy.tabular.manifest.Manifest (built-in class) nipoppy.tabular.manifest.ManifestModel (built-in class) nipoppy.utils module nipoppy.workflows module nipoppy.workflows.base module nipoppy.workflows.base.BaseWorkflow (built-in class) nipoppy.workflows.BasePipelineWorkflow (built-in class) nipoppy.workflows.BaseWorkflow (built-in class) nipoppy.workflows.bids_conversion module nipoppy.workflows.bids_conversion.BidsConversionRunner (built-in class) nipoppy.workflows.BidsConversionRunner (built-in class) nipoppy.workflows.dataset_init module nipoppy.workflows.dataset_init.InitWorkflow (built-in class) nipoppy.workflows.dataset_status module nipoppy.workflows.dataset_status.StatusWorkflow (built-in class) nipoppy.workflows.dicom_reorg module nipoppy.workflows.dicom_reorg.DicomReorgWorkflow (built-in class) nipoppy.workflows.DicomReorgWorkflow (built-in class) nipoppy.workflows.doughnut module nipoppy.workflows.doughnut.DoughnutWorkflow (built-in class) nipoppy.workflows.DoughnutWorkflow (built-in class) nipoppy.workflows.ExtractionRunner (built-in class) nipoppy.workflows.extractor module nipoppy.workflows.extractor.ExtractionRunner (built-in class) nipoppy.workflows.InitWorkflow (built-in class) nipoppy.workflows.pipeline module nipoppy.workflows.pipeline.BasePipelineWorkflow (built-in class) nipoppy.workflows.PipelineRunner (built-in class) nipoppy.workflows.PipelineTracker (built-in class) nipoppy.workflows.runner module nipoppy.workflows.runner.PipelineRunner (built-in class) nipoppy.workflows.tracker module nipoppy.workflows.tracker.PipelineTracker (built-in class) P parser (in module script) PARTIAL_SUCCESS (nipoppy.env.LogColor attribute) (nipoppy.env.ReturnCode attribute) participant (nipoppy.config.pipeline_step.AnalysisLevelType attribute) participant_dicom_dir (nipoppy.tabular.dicom_dir_map.DicomDirMapModel attribute) (nipoppy.tabular.doughnut.DoughnutModel attribute) participant_id (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMapModel attribute) (nipoppy.tabular.manifest.ManifestModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) participant_id_to_bids_participant_id() (in module nipoppy.utils) participant_session (nipoppy.config.pipeline_step.AnalysisLevelType attribute) path (nipoppy.layout.PathInfo attribute) path_infos (nipoppy.layout.LayoutConfig property) path_labels (nipoppy.layout.LayoutConfig property) path_sep (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) PATHS (nipoppy.config.tracker.TrackerConfig attribute) (nipoppy.config.TrackerConfig attribute) pipeline_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) pipeline_name (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) pipeline_step (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) pipeline_step_config (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.bids_conversion.BidsConversionRunner property) (nipoppy.workflows.BidsConversionRunner property) (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) pipeline_version (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) prepare_container() (in module nipoppy.config.container) PROC_DEPENDENCIES (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) proc_pipeline_info (nipoppy.workflows.ExtractionRunner property) (nipoppy.workflows.extractor.ExtractionRunner property) PROC_PIPELINES (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) process_container_config() (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.runner.PipelineRunner method) process_template_json() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) process_template_str() (in module nipoppy.utils) propagate_container_config() (nipoppy.config.Config method) (nipoppy.config.main.Config method) PYBIDS_IGNORE_FILE (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) pybids_ignore_patterns (nipoppy.workflows.BasePipelineWorkflow property) (nipoppy.workflows.pipeline.BasePipelineWorkflow property) PyPI R regenerate (nipoppy.workflows.doughnut.DoughnutWorkflow attribute) (nipoppy.workflows.DoughnutWorkflow attribute) return_code (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) rm() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) run() (in module script) (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) run_cleanup() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.doughnut.DoughnutWorkflow method) (nipoppy.workflows.DoughnutWorkflow method) (nipoppy.workflows.InitWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) run_command() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) run_main() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.dataset_init.InitWorkflow method) (nipoppy.workflows.dataset_status.StatusWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.doughnut.DoughnutWorkflow method) (nipoppy.workflows.DoughnutWorkflow method) (nipoppy.workflows.InitWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) run_multi() (in module script) run_setup() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.BaseWorkflow method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.tracker.PipelineTracker method) run_single() (in module script) (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.bids_conversion.BidsConversionRunner method) (nipoppy.workflows.BidsConversionRunner method) (nipoppy.workflows.dicom_reorg.DicomReorgWorkflow method) (nipoppy.workflows.DicomReorgWorkflow method) (nipoppy.workflows.ExtractionRunner method) (nipoppy.workflows.extractor.ExtractionRunner method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) (nipoppy.workflows.PipelineRunner method) (nipoppy.workflows.PipelineTracker method) (nipoppy.workflows.runner.PipelineRunner method) (nipoppy.workflows.tracker.PipelineTracker method) run_single_qc() (in module script) run_single_stats() (in module script) S save() (nipoppy.config.Config method) (nipoppy.config.main.Config method) save_df_with_backup() (in module nipoppy.utils) save_json() (in module nipoppy.utils) save_tabular_file() (nipoppy.workflows.base.BaseWorkflow method) (nipoppy.workflows.BaseWorkflow method) save_with_backup() (nipoppy.tabular.base.BaseTabular method) script module sep (nipoppy.tabular.base.BaseTabular attribute) session (nipoppy.config.pipeline_step.AnalysisLevelType attribute) Session ID session_id (nipoppy.tabular.bagel.BagelModel attribute) (nipoppy.tabular.dicom_dir_map.DicomDirMapModel attribute) (nipoppy.tabular.manifest.ManifestModel attribute) (nipoppy.workflows.BasePipelineWorkflow attribute) (nipoppy.workflows.pipeline.BasePipelineWorkflow attribute) session_id_to_bids_session_id() (in module nipoppy.utils) SESSION_IDS (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) session_ids (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) SESSIONS set_container_env_vars() (in module nipoppy.config.container) set_status() (nipoppy.tabular.Doughnut method) (nipoppy.tabular.doughnut.Doughnut method) set_up_bids_db() (nipoppy.workflows.BasePipelineWorkflow method) (nipoppy.workflows.pipeline.BasePipelineWorkflow method) simulate (nipoppy.workflows.PipelineRunner attribute) (nipoppy.workflows.runner.PipelineRunner attribute) sort_values() (nipoppy.tabular.base.BaseTabular method) status (nipoppy.tabular.bagel.BagelModel attribute) status_cols (nipoppy.tabular.Doughnut attribute) (nipoppy.tabular.doughnut.Doughnut attribute) STATUS_FAIL (in module nipoppy.tabular.bagel) status_fail (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) STATUS_INCOMPLETE (in module nipoppy.tabular.bagel) status_incomplete (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) STATUS_SUCCESS (in module nipoppy.tabular.bagel) status_success (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) STATUS_UNAVAILABLE (in module nipoppy.tabular.bagel) status_unavailable (nipoppy.tabular.Bagel attribute) (nipoppy.tabular.bagel.Bagel attribute) STEP (nipoppy.config.pipeline.PipelineInfo attribute) STEPS (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.BidsPipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline.BidsPipelineConfig attribute) (nipoppy.config.pipeline.ExtractionPipelineConfig attribute) (nipoppy.config.pipeline.ProcPipelineConfig attribute) (nipoppy.config.ProcPipelineConfig attribute) StrOrPathLike (in module nipoppy.env) SUBSTITUTIONS (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) SUCCESS (nipoppy.env.LogColor attribute) (nipoppy.env.ReturnCode attribute) T TEMPLATE_REPLACE_PATTERN (in module nipoppy.utils) TRACKER_CONFIG_FILE (nipoppy.config.pipeline.ProcPipelineConfig attribute) (nipoppy.config.pipeline_step.ProcPipelineStepConfig attribute) (nipoppy.config.ProcPipelineConfig attribute) (nipoppy.config.ProcPipelineStepConfig attribute) U UPDATE_DOUGHNUT (nipoppy.config.BidsPipelineStepConfig attribute) (nipoppy.config.pipeline_step.BidsPipelineStepConfig attribute) update_doughnut() (in module nipoppy.tabular) (in module nipoppy.tabular.doughnut) URI (nipoppy.config.container.ContainerInfo attribute) V validate() (nipoppy.layout.DatasetLayout method) (nipoppy.tabular.base.BaseTabular method) (nipoppy.tabular.Manifest method) (nipoppy.tabular.manifest.Manifest method) validate_after() (nipoppy.config.BasePipelineConfig method) (nipoppy.config.pipeline.BasePipelineConfig method) (nipoppy.config.pipeline.ExtractionPipelineConfig method) (nipoppy.config.pipeline_step.ProcPipelineStepConfig method) (nipoppy.config.ProcPipelineStepConfig method) (nipoppy.config.tracker.TrackerConfig method) (nipoppy.config.TrackerConfig method) (nipoppy.tabular.bagel.BagelModel method) (nipoppy.tabular.dicom_dir_map.DicomDirMapModel method) (nipoppy.tabular.manifest.ManifestModel method) validate_and_process() (nipoppy.config.Config method) (nipoppy.config.main.Config method) validate_before() (nipoppy.config.BasePipelineConfig class method) (nipoppy.config.BasePipelineStepConfig class method) (nipoppy.config.pipeline.BasePipelineConfig class method) (nipoppy.config.pipeline_step.BasePipelineStepConfig class method) (nipoppy.tabular.bagel.BagelModel class method) (nipoppy.tabular.base.BaseTabularModel class method) validate_layout (nipoppy.workflows.base.BaseWorkflow attribute) (nipoppy.workflows.BaseWorkflow attribute) (nipoppy.workflows.dataset_init.InitWorkflow attribute) (nipoppy.workflows.InitWorkflow attribute) venv VERSION (nipoppy.config.BasePipelineConfig attribute) (nipoppy.config.pipeline.BasePipelineConfig attribute) (nipoppy.config.pipeline.PipelineInfo attribute) Visit ID visit_id (nipoppy.tabular.manifest.ManifestModel attribute) VISIT_IDS (nipoppy.config.Config attribute) (nipoppy.config.main.Config attribute) visit_ids (nipoppy.tabular.Manifest attribute) (nipoppy.tabular.manifest.Manifest attribute) VISITS