Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W _ __init__() (thesis.cli.ClickNodeProgress method) (thesis.core.config.manager.ConfigManager method) (thesis.core.context.ProcessingContext method) (thesis.core.nipype.executor.NipypeExecutor method) (thesis.core.nipype.executor.NipypeStatusCallback method) (thesis.core.output.events.Event method) (thesis.core.output.events.EventBus method) (thesis.core.output.progress.NodeProgressProtocol method) (thesis.core.output.renderer.OutputRenderer method) (thesis.core.path_declarations.CohortDir method) (thesis.core.path_declarations.CohortPatient method) (thesis.core.path_declarations.CohortPatients method) (thesis.core.path_declarations.ConfigList method) (thesis.core.path_declarations.ConfigListItem method) (thesis.core.path_declarations.DataDir method) (thesis.core.path_declarations.DataFile method) (thesis.core.path_declarations.ExternalFile method) (thesis.core.path_declarations.GlobGroup method) (thesis.core.path_declarations.GlobGroupResult method) (thesis.core.path_declarations.GlobMatch method) (thesis.core.path_declarations.OutputDir method) (thesis.core.path_declarations.PatientDir method) (thesis.core.path_declarations.PatientFile method) (thesis.core.path_declarations.PriorOutput method) (thesis.core.path_declarations.WorkingFile method) (thesis.core.registry.WorkflowEntry method) (thesis.core.registry.WorkflowRegistry method) (thesis.workflows.atlas._params.AtlasParams method) (thesis.workflows.atlas.compute.QcParams method) (thesis.workflows.full_pipeline._core.BackendDescriptor method) (thesis.workflows.full_pipeline._core.CoreScaffold method) (thesis.workflows.mrtrix3.workflow.SharedSubgraph method) (thesis.workflows.registration.paths.ResolvedRegistrationJob method) __new__() (thesis.core.config.validators.NormalizationMethod method) (thesis.core.gpu.GPUStatus static method) (thesis.core.output.events.EventLevel method) (thesis.core.output.modes.OutputFormat method) (thesis.core.output.modes.OutputMode method) (thesis.core.output.modes.SummaryDetail method) (thesis.core.output.summary.RunStatus method) A acq_params (thesis.core.config.validators.PreprocessingConfig attribute) (thesis.workflows.preprocess.config.PreprocessConfig attribute) AcqParamsConfig (class in thesis.workflows.preprocess.config) adapt_tckgen_inputs_task() (in module thesis.workflows.mrtrix3.operations.tckgen_adapter) add_metadata() (thesis.core.context.ProcessingContext method) add_result() (thesis.core.context.ProcessingContext method) affine_iterations (thesis.core.config.validators.FireantsRegistrationConfig attribute) affine_lr (thesis.core.config.validators.FireantsRegistrationConfig attribute) affine_native_relpath (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) aggregation (thesis.core.config.validators.TractSimilaritySweepConfig attribute) all_entries() (thesis.core.registry.WorkflowRegistry method) apply_nipype_execution_config() (in module thesis.core.nipype.executor) apply_preproc_override() (in module thesis.workflows.full_pipeline._core) apply_threshold() (in module thesis.workflows.tract_similarity.workflow) apply_transform_ants() (in module thesis.workflows.transforms.operations) assets_dir (thesis.core.config.validators.PathConfig attribute) atlas (thesis.core.config.validators.PipelineConfig attribute) atlas_qc (thesis.core.config.validators.PipelineConfig attribute) atlas_relpath (thesis.core.config.validators.TractSimilarityConfig attribute) atlas_sources (thesis.core.config.validators.TractographyConfig attribute) atlas_threshold (thesis.core.config.validators.TractSimilarityConfig attribute) atlas_threshold_grid (thesis.core.config.validators.TractSimilaritySweepConfig attribute) atlas_to_patient_wf (thesis.workflows.full_pipeline._core.CoreScaffold attribute) atlas_transforms (thesis.core.config.validators.TransformsConfig attribute) AtlasConfig (class in thesis.core.config.validators) AtlasParams (class in thesis.workflows.atlas._params) AtlasQCConfig (class in thesis.core.config.validators) AtlasSourceConfig (class in thesis.core.config.validators) AtlasTransformConfig (class in thesis.core.config.validators) attach() (thesis.core.output.renderer.OutputRenderer method) attach_inputnode() (in module thesis.core.contracts) attach_outputnode() (in module thesis.core.contracts) auto_open (thesis.core.config.validators.RegistrationViewerConfig attribute) available (thesis.core.gpu.GPUStatus attribute) avg_elapsed_seconds (thesis.core.output.summary.BatchSummary attribute) B backend (thesis.core.config.validators.RegistrationViewerConfig attribute) BackendDescriptor (class in thesis.workflows.full_pipeline._core) bandwidth (thesis.workflows.preprocess.config.AcqParamsConfig attribute) base_dir (thesis.core.config.validators.TransformsConfig attribute) base_dirs (thesis.core.path_declarations.ExternalFile attribute) BaseConfig (class in thesis.core.config.validators) batch_size (thesis.workflows.learned_atlas._params.LearnedAtlasOptimizerConfig attribute) BatchSummary (class in thesis.core.output.summary) bedpostx (thesis.workflows.preprocess.config.PreprocessConfig attribute) bedpostx_dir (thesis.core.config.validators.HCPConfig attribute) (thesis.workflows.hcp.config.paths.HCPPaths attribute) (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) BedpostXConfig (class in thesis.workflows.preprocess.config) bet (thesis.workflows.preprocess.config.PreprocessConfig attribute) BetConfig (class in thesis.workflows.preprocess.config) bias_correction (thesis.core.config.validators.PreprocessingConfig attribute) binary (thesis.core.gpu.GPUStatus attribute) binary_merge_rois_task() (in module thesis.workflows.hcp.operations.merging) blocked (thesis.core.output.summary.BatchSummary attribute) BLOCKED (thesis.core.output.summary.RunStatus attribute) brain_extraction (thesis.core.config.validators.PreprocessingConfig attribute) brain_extraction_method (thesis.core.config.validators.PreprocessingConfig attribute) bucket (thesis.core.config.validators.S3Config attribute) build_bullets() (in module thesis.core.output.summary) build_cohort_workflow() (in module thesis.workflows.tract_similarity.workflow) build_fireants_node() (in module thesis.workflows.registration.fireants_backend) build_fsleyes_command() (in module thesis.workflows.registration.viewers) build_nipype_status_callback() (in module thesis.core.nipype.executor) build_occupancy_map() (in module thesis.workflows.atlas.qc_metrics) build_output_filename() (in module thesis.workflows.transforms.operations) build_sweep_workflow() (in module thesis.workflows.tract_similarity.sweep) build_validation_workflow() (in module thesis.workflows.tract_synthseg.validation) build_workflow() (in module thesis.workflows.atlas.workflow) (in module thesis.workflows.atlas_to_patient.workflow) (in module thesis.workflows.full_pipeline.workflow) (in module thesis.workflows.hcp.workflow) (in module thesis.workflows.learned_atlas.workflow) (in module thesis.workflows.minimal) (in module thesis.workflows.mrtrix3.workflow) (in module thesis.workflows.preprocess.workflow) (in module thesis.workflows.qc.workflow) (in module thesis.workflows.registration.workflow) (in module thesis.workflows.synthseg.workflow) (in module thesis.workflows.tract_similarity.hcp_loo) (in module thesis.workflows.tract_similarity.workflow) (in module thesis.workflows.tract_synthseg.workflow) (in module thesis.workflows.transforms.workflow) bullets (thesis.core.output.summary.RunSummary attribute) burn_in (thesis.workflows.preprocess.config.BedpostXConfig attribute) bval (thesis.workflows.mrtrix3.config.paths.MRtrix3Paths attribute) bvec (thesis.workflows.mrtrix3.config.paths.MRtrix3Paths attribute) C cache_policy (thesis.core.config.validators.S3Config attribute) category (thesis.core.output.events.Event attribute) cc_kernel_size (thesis.core.config.validators.FireantsRegistrationConfig attribute) centroid_scatter() (in module thesis.workflows.learned_atlas.diagnostics) channels (thesis.workflows.learned_atlas._params.LearnedAtlasModelConfig attribute) check_file_exists() (in module thesis.core.io) check_gpu() (in module thesis.core.gpu) check_rois (thesis.core.config.validators.ValidationConfig attribute) cleanup() (thesis.core.nipype.executor.NipypeExecutor method) cleanup_working_dir() (thesis.core.context.ProcessingContext method) clear() (thesis.core.output.events.EventBus method) clear_cache() (thesis.core.config.manager.ConfigManager method) ClickNodeProgress (class in thesis.cli) cohort_output_subdir (thesis.core.config.validators.TractSimilarityConfig attribute) CohortDir (class in thesis.core.path_declarations) CohortPatient (class in thesis.core.path_declarations) CohortPatients (class in thesis.core.path_declarations) collapse_output_transforms (thesis.core.config.validators.RegistrationConfig attribute) (thesis.workflows.preprocess.config.RegistrationStepConfig attribute) collect_batch_stats() (in module thesis.workflows.qc.statistics) collect_connectivity_map_stats() (in module thesis.workflows.qc.checks) collect_tractography_stats() (in module thesis.workflows.qc.statistics) commands_run (thesis.core.output.summary.RunResult attribute) COMPACT (thesis.core.output.modes.SummaryDetail attribute) compute_atlas_statistics() (in module thesis.workflows.atlas._statistics) compute_cv (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.workflows.atlas.compute.QcParams attribute) compute_jacobian_stats() (in module thesis.workflows.qc.checks) compute_kurt (thesis.workflows.preprocess.config.DTIFitConfig attribute) compute_leave_one_out_dice() (in module thesis.workflows.atlas.qc_metrics) compute_log_stats (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.workflows.atlas.compute.QcParams attribute) compute_map_coefficient_of_variation() (in module thesis.workflows.atlas.qc_metrics) compute_subject_dice_against_core() (in module thesis.workflows.atlas.qc_metrics) config (thesis.core.context.ProcessingContext attribute) config_path (thesis.core.path_declarations.ConfigList attribute) (thesis.core.path_declarations.ExternalFile attribute) (thesis.core.path_declarations.PatientDir attribute) (thesis.core.path_declarations.PatientFile attribute) config_paths (thesis.core.path_declarations.ExternalFile attribute) (thesis.core.path_declarations.PatientDir attribute) (thesis.core.path_declarations.PatientFile attribute) ConfigList (class in thesis.core.path_declarations) ConfigListItem (class in thesis.core.path_declarations) ConfigManager (class in thesis.core.config.manager) ConfigurationError convert_synthseg_to_gm_wm_csf() (in module thesis.workflows.preprocess.operations.label_ops) convert_to_path() (thesis.core.config.validators.PathConfig class method) copy_nifti_metadata() (in module thesis.core.io) CoreScaffold (class in thesis.workflows.full_pipeline._core) correlation_metrics() (in module thesis.workflows.tract_similarity._metrics) count_negative_jacobians() (in module thesis.workflows.learned_atlas.model) count_workflow_nodes() (in module thesis.core.nipype.executor) cov_mean_threshold_pct (thesis.core.config.validators.AtlasConfig attribute) (thesis.workflows.atlas._params.AtlasParams attribute) cpu (thesis.core.config.validators.SynthSegConfig attribute) (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) crash_dir (thesis.core.config.validators.NipypeConfig attribute) create_acqparams_file() (in module thesis.workflows.preprocess.operations.file_ops) create_context() (in module thesis.core.context) create_hcp_output_structure() (in module thesis.workflows.preprocess.operations.file_ops) create_index_file() (in module thesis.workflows.preprocess.operations.file_ops) create_masks (thesis.core.config.validators.SegmentationConfig attribute) create_tractography_masks() (in module thesis.workflows.preprocess.operations.label_ops) crop (thesis.core.config.validators.SynthSegConfig attribute) (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) cuda_version (thesis.core.gpu.GPUStatus attribute) curvature_threshold (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) cv_mean_threshold (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.workflows.atlas.compute.QcParams attribute) D data_dir (thesis.core.context.ProcessingContext attribute) DataDir (class in thesis.core.path_declarations) DataFile (class in thesis.core.path_declarations) DEBUG (thesis.core.output.events.EventLevel attribute) dec_features (thesis.workflows.learned_atlas._params.LearnedAtlasModelConfig attribute) default (thesis.core.path_declarations.PatientDir attribute) (thesis.core.path_declarations.PatientFile attribute) default_config (thesis.core.registry.WorkflowEntry attribute) DEFAULT_COV_MEAN_THRESHOLD_PCT (in module thesis.workflows.atlas._params) DEFAULT_INT_STEPS (in module thesis.workflows.learned_atlas._params) DEFAULT_LOG_OFFSET (in module thesis.workflows.learned_atlas._params) DEFAULT_NORMALIZATION_METHOD (in module thesis.workflows.atlas._params) DEFAULT_PRESENCE_VALUE (in module thesis.workflows.atlas._params) default_protocol (thesis.core.registry.WorkflowEntry attribute) DEFAULT_REGISTRATION_JOB (in module thesis.workflows.registration.paths) deform_algo (thesis.core.config.validators.FireantsRegistrationConfig attribute) deformable_iterations (thesis.core.config.validators.FireantsRegistrationConfig attribute) deformable_lr (thesis.core.config.validators.FireantsRegistrationConfig attribute) deformable_max_spacing_mm (thesis.core.config.validators.FireantsRegistrationConfig attribute) deformation_type (thesis.core.config.validators.FireantsRegistrationConfig attribute) delta_on_true_support() (in module thesis.workflows.learned_atlas.diagnostics) denoise (thesis.core.config.validators.PreprocessingConfig attribute) DependencyError describe_registration_viewer_command() (in module thesis.workflows.registration.viewers) description (thesis.core.registry.WorkflowEntry attribute) detach() (thesis.core.output.renderer.OutputRenderer method) detect_batch_outliers() (in module thesis.workflows.qc.checks) device (thesis.core.config.validators.FireantsRegistrationConfig attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) dice_score() (in module thesis.workflows.atlas.qc_metrics) diffusion_dir (thesis.core.config.validators.HCPConfig attribute) (thesis.workflows.hcp.config.paths.HCPPaths attribute) (thesis.workflows.mrtrix3.config.paths.MRtrix3Paths attribute) (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) dir_fields (thesis.core.path_declarations.ConfigList attribute) direction (thesis.core.config.validators.TransformJobConfig attribute) dirname (thesis.core.path_declarations.DataDir attribute) discover_patient_dirs() (in module thesis.workflows.tract_similarity._io) discover_roi_files() (in module thesis.workflows.qc.operations) dist_thresh (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) distance_metrics() (in module thesis.workflows.tract_similarity._metrics) distribution_metrics() (in module thesis.workflows.tract_similarity._metrics) do_moments (thesis.core.config.validators.FireantsRegistrationConfig attribute) do_rigid (thesis.core.config.validators.FireantsRegistrationConfig attribute) driver (thesis.core.config.validators.FireantsRegistrationConfig attribute) dtifit (thesis.workflows.preprocess.config.PreprocessConfig attribute) DTIFitConfig (class in thesis.workflows.preprocess.config) dtype (thesis.core.config.validators.FireantsRegistrationConfig attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) dwi_ap (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) dwi_ap_bval (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) dwi_ap_bvec (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) dwi_image (thesis.workflows.mrtrix3.config.paths.MRtrix3Paths attribute) dwi_import_node (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) dwi_pa (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) dwi_to_t1 (thesis.workflows.preprocess.config.RegistrationChainConfig attribute) E eddy_correction (thesis.core.config.validators.PreprocessingConfig attribute) elapsed_seconds (thesis.core.output.summary.RunResult attribute) (thesis.core.output.summary.RunSummary attribute) emit() (thesis.core.logging.handlers.InterceptHandler method) (thesis.core.logging.InterceptHandler method) (thesis.core.output.events.EventBus method) emit_baseline_maps (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) emit_event() (thesis.core.output.events.EventBus method) emit_heatmap (thesis.core.config.validators.TractSimilaritySweepConfig attribute) enabled (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationViewerConfig attribute) (thesis.core.config.validators.S3Config attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) enc_features (thesis.workflows.learned_atlas._params.LearnedAtlasModelConfig attribute) ensure_directory() (in module thesis.core.io) epochs (thesis.workflows.learned_atlas._params.LearnedAtlasOptimizerConfig attribute) ERROR (thesis.core.output.events.EventLevel attribute) error_history (thesis.core.output.summary.RunResult attribute) error_message (thesis.core.output.summary.RunResult attribute) error_type (thesis.core.output.summary.RunResult attribute) evaluate_prediction() (in module thesis.workflows.learned_atlas.diagnostics) Event (class in thesis.core.output.events) event_count (thesis.core.output.events.EventBus property) EventBus (class in thesis.core.output.events) EventLevel (class in thesis.core.output.events) exclude (thesis.core.path_declarations.CohortPatients attribute) execute() (thesis.core.nipype.executor.NipypeExecutor method) existence_errors() (thesis.core.path_declarations.CohortPatients method) (thesis.core.path_declarations.ConfigList method) (thesis.core.path_declarations.DataDir method) (thesis.core.path_declarations.DataFile method) (thesis.core.path_declarations.ExternalFile method) (thesis.core.path_declarations.GlobGroup method) (thesis.core.path_declarations.GlobMatch method) (thesis.core.path_declarations.PathDeclaration method) (thesis.core.path_declarations.PatientDir method) (thesis.core.path_declarations.PatientFile method) (thesis.core.path_declarations.PriorOutput method) ExternalFile (class in thesis.core.path_declarations) extract_rois_task() (in module thesis.workflows.hcp.operations.extraction) F factory (thesis.core.registry.WorkflowEntry attribute) failed (thesis.core.output.summary.BatchSummary attribute) FAILED (thesis.core.output.summary.RunStatus attribute) failed_nodes (thesis.core.nipype.executor.NipypeStatusCallback property) failure_reasons (thesis.core.output.summary.BatchSummary attribute) fallback_dirs (thesis.core.path_declarations.ConfigList attribute) (thesis.core.path_declarations.GlobGroup attribute) (thesis.core.path_declarations.GlobMatch attribute) (thesis.core.path_declarations.PatientDir attribute) (thesis.core.path_declarations.PatientFile attribute) (thesis.core.path_declarations.PriorOutput attribute) fan_out() (in module thesis.core.contracts) fast (thesis.core.config.validators.SynthSegConfig attribute) (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) fdt_name (thesis.core.config.validators.TractSimilarityConfig attribute) fibst (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) file_fields (thesis.core.path_declarations.ConfigList attribute) file_patterns (thesis.core.path_declarations.CohortPatients attribute) FileIOError filename (thesis.core.path_declarations.DataFile attribute) (thesis.core.path_declarations.PriorOutput attribute) files_changed (thesis.core.output.summary.RunResult attribute) finalize_tract_similarity_merge() (in module thesis.workflows.full_pipeline._core) find_files() (in module thesis.core.io) finished_ok_nodes (thesis.core.nipype.executor.NipypeStatusCallback property) fireants (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) FireantsRegistrationConfig (class in thesis.core.config.validators) fivett_algorithm (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) fivett_node (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) fivett_t1_node (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) fixed_image (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) fod_algorithm (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) fod_node (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) force_dir (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) format_duration() (in module thesis.core.output.summary) format_stats_table() (in module thesis.workflows.qc.statistics) frac_dwi (thesis.workflows.preprocess.config.BetConfig attribute) frac_t1 (thesis.workflows.preprocess.config.BetConfig attribute) frac_t2 (thesis.workflows.preprocess.config.BetConfig attribute) from_dict() (thesis.core.config.validators.PipelineConfig class method) from_registration (thesis.core.config.validators.TransformJobConfig attribute) from_result() (thesis.core.output.summary.RunSummary class method) from_results() (thesis.core.output.summary.BatchSummary class method) fsamples (thesis.workflows.hcp.config.paths.HCPPaths attribute) FULL (thesis.core.output.modes.SummaryDetail attribute) G generate_atlas_with_qc() (in module thesis.workflows.atlas.compute) generate_bedpostx_overlay() (in module thesis.workflows.qc.checks) generate_brain_mask_overlay() (in module thesis.workflows.qc.checks) generate_connectivity_map_figures() (in module thesis.workflows.qc.checks) generate_dwi2mask_task() (in module thesis.workflows.mrtrix3.operations.mask_prep) generate_group_plots (thesis.core.config.validators.AtlasQCConfig attribute) generate_overlays (thesis.core.config.validators.QCConfig attribute) generate_patient_reports (thesis.core.config.validators.AtlasQCConfig attribute) generate_roi_overlays() (in module thesis.workflows.qc.roi_overlay) generate_roi_transform_comparison() (in module thesis.workflows.qc.checks) generate_statistical_atlas() (in module thesis.workflows.atlas.compute) generate_synthseg_overlay() (in module thesis.workflows.qc.checks) generate_track_density_figures() (in module thesis.workflows.qc.track_density) generate_waytotal_overlay() (in module thesis.workflows.qc.checks) get() (thesis.core.registry.WorkflowRegistry method) get_config_dir() (thesis.core.config.manager.ConfigManager method) get_console_format() (in module thesis.core.logging.formatters) get_event_bus() (in module thesis.core.output.events) get_events() (thesis.core.output.events.EventBus method) get_file_format() (in module thesis.core.logging.formatters) get_file_info() (in module thesis.core.io) get_input_path() (thesis.core.context.ProcessingContext method) get_logger() (in module thesis.core.logging) get_metadata() (thesis.core.context.ProcessingContext method) get_output_path() (thesis.core.context.ProcessingContext method) get_probtrackx2_interface() (in module thesis.core.nipype.interfaces.fsl) get_registration_inverse_warped_image_path() (in module thesis.workflows.registration.paths) get_registration_job_dir() (in module thesis.workflows.registration.paths) get_registration_job_inverse_warped_image_path() (in module thesis.workflows.registration.paths) get_registration_job_transform_dir() (in module thesis.workflows.registration.paths) get_registration_job_transform_paths() (in module thesis.workflows.registration.paths) get_registration_job_warped_image_path() (in module thesis.workflows.registration.paths) get_registration_output_dir() (in module thesis.workflows.registration.paths) get_registration_transform_dir() (in module thesis.workflows.registration.paths) get_registration_transform_prefix() (in module thesis.workflows.registration.paths) get_registration_warped_image_path() (in module thesis.workflows.registration.paths) get_result() (thesis.core.context.ProcessingContext method) get_transform_type_from_paths() (in module thesis.workflows.transforms.operations) get_working_directory() (thesis.core.nipype.executor.NipypeExecutor method) get_working_path() (thesis.core.context.ProcessingContext method) glob_pattern (thesis.core.path_declarations.PriorOutput attribute) GlobGroup (class in thesis.core.path_declarations) GlobGroupResult (class in thesis.core.path_declarations) GlobMatch (class in thesis.core.path_declarations) gmwmi_apply_roi_filters (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) gmwmi_node (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) gpu_device (thesis.core.config.validators.HardwareConfig attribute) gpu_enabled (thesis.core.config.validators.HardwareConfig attribute) gpu_runtime_env (thesis.core.config.validators.SynthSegConfig attribute) (thesis.core.config.validators.TractographyConfig attribute) GPUStatus (class in thesis.core.gpu) group_core_threshold (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.workflows.atlas.compute.QcParams attribute) H hardware (thesis.core.config.validators.PipelineConfig attribute) HardwareConfig (class in thesis.core.config.validators) has() (thesis.core.registry.WorkflowRegistry method) has_result() (thesis.core.context.ProcessingContext method) hash_method (thesis.core.config.validators.NipypeConfig attribute) hcp (thesis.core.config.validators.PipelineConfig attribute) hcp_loo (thesis.core.config.validators.TractSimilarityConfig attribute) HCPConfig (class in thesis.core.config.validators) HcpLooConfig (class in thesis.core.config.validators) HCPPaths (class in thesis.workflows.hcp.config.paths) headline (thesis.core.output.summary.RunSummary attribute) hemisphere (thesis.core.config.validators.TractographyConfig attribute) HUMAN (thesis.core.output.modes.OutputFormat attribute) I IMPORTANT (thesis.core.output.events.EventLevel attribute) INFO (thesis.core.output.events.EventLevel attribute) input_dir (thesis.core.context.ProcessingContext attribute) (thesis.workflows.hcp.config.paths.HCPPaths attribute) (thesis.workflows.mrtrix3.config.paths.MRtrix3Paths attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) input_files (thesis.core.config.validators.TransformJobConfig attribute) input_spec (thesis.core.nipype.interfaces.freesurfer.SynthSeg attribute) (thesis.core.nipype.interfaces.freesurfer.SynthStrip attribute) (thesis.core.nipype.interfaces.fsl.ProbTrackX2GPU attribute) inputs_dir (thesis.core.config.validators.PathConfig attribute) int_steps (thesis.workflows.learned_atlas._params.LearnedAtlasModelConfig attribute) InterceptHandler (class in thesis.core.logging) (class in thesis.core.logging.handlers) interpolation (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.core.config.validators.TransformJobConfig attribute) (thesis.workflows.preprocess.config.LabelTransformConfig attribute) (thesis.workflows.preprocess.config.RegistrationStepConfig attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) inverse_max_iterations (thesis.core.config.validators.FireantsRegistrationConfig attribute) inverse_method (thesis.core.config.validators.FireantsRegistrationConfig attribute) inverse_tolerance (thesis.core.config.validators.FireantsRegistrationConfig attribute) inverse_warp_streamlines_task() (in module thesis.workflows.hcp.operations.streamline_warping) is_cohort_level (thesis.core.registry.WorkflowEntry attribute) is_default (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) is_json (thesis.core.output.modes.OutputConfig property) is_multi_tissue (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) is_quiet (thesis.core.output.modes.OutputConfig property) is_verbose (thesis.core.output.modes.OutputConfig property) items (thesis.core.path_declarations.GlobGroup attribute) J jacobian_determinant() (in module thesis.workflows.learned_atlas.model) jacobian_min_and_folds() (in module thesis.workflows.learned_atlas.train) jobs (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.TransformsConfig attribute) JSON (thesis.core.output.modes.OutputFormat attribute) K keep_inputs (thesis.core.config.validators.NipypeConfig attribute) L label_file (thesis.core.config.validators.AtlasSourceConfig attribute) label_transform (thesis.workflows.preprocess.config.PreprocessConfig attribute) labels (thesis.core.config.validators.SegmentationConfig attribute) LabelTransformConfig (class in thesis.workflows.preprocess.config) launch_registration_viewer() (in module thesis.workflows.registration.viewers) learned_prediction_relpath (thesis.core.config.validators.HcpLooConfig attribute) learned_support_threshold (thesis.core.config.validators.HcpLooConfig attribute) LearnedAtlasConfig (class in thesis.workflows.learned_atlas._params) LearnedAtlasLossConfig (class in thesis.workflows.learned_atlas._params) LearnedAtlasModelConfig (class in thesis.workflows.learned_atlas._params) LearnedAtlasOptimizerConfig (class in thesis.workflows.learned_atlas._params) leave_one_out (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.workflows.atlas.compute.QcParams attribute) leave_one_out_min_subjects (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.workflows.atlas.compute.QcParams attribute) level (thesis.core.output.events.Event attribute) list() (thesis.core.registry.WorkflowRegistry method) list_configs() (thesis.core.config.manager.ConfigManager method) list_input_files() (thesis.core.context.ProcessingContext method) list_output_files() (thesis.core.context.ProcessingContext method) load_atlas_normalized() (in module thesis.workflows.tract_similarity._io) load_bvals() (in module thesis.core.io) load_bvecs() (in module thesis.core.io) load_config() (thesis.core.config.manager.ConfigManager method) load_config_dict() (thesis.core.config.manager.ConfigManager method) load_fdt_paths_normalized() (in module thesis.workflows.tract_similarity._io) load_nifti() (in module thesis.core.io) load_probtrackx_volume() (in module thesis.workflows.tract_similarity._io) load_yaml() (in module thesis.core.config.loaders) log_dir (thesis.core.config.validators.PathConfig attribute) log_offset (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.workflows.atlas.compute.QcParams attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasLossConfig attribute) loop_check (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) loss (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) loss_type (thesis.core.config.validators.FireantsRegistrationConfig attribute) lr (thesis.workflows.learned_atlas._params.LearnedAtlasOptimizerConfig attribute) M make_ants_apply_transforms_interface() (in module thesis.workflows.preprocess.nodes.registration) mask_dilate_voxels (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) mask_from_dwi (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) mask_name (thesis.core.config.validators.HCPConfig attribute) mask_node (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) mask_path (thesis.core.config.validators.HCPConfig attribute) (thesis.workflows.hcp.config.paths.HCPPaths attribute) (thesis.workflows.mrtrix3.config.paths.MRtrix3Paths attribute) mask_source (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) mass_matched_residual_fraction() (in module thesis.workflows.learned_atlas.diagnostics) MAX (thesis.core.config.validators.NormalizationMethod attribute) max_retries (thesis.core.config.validators.S3Config attribute) mem_gb_cpu (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) mem_gb_gpu (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) memory_gb (thesis.core.config.validators.HardwareConfig attribute) merge_configs() (in module thesis.core.config.loaders) merge_rois_task() (in module thesis.workflows.hcp.operations.merging) merge_with() (thesis.core.config.validators.PipelineConfig method) message (thesis.core.output.events.Event attribute) meta (thesis.workflows.full_pipeline._core.CoreScaffold attribute) metadata (thesis.core.context.ProcessingContext attribute) (thesis.core.output.events.Event attribute) (thesis.core.output.summary.RunResult attribute) method (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.core.config.validators.SegmentationConfig attribute) (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.preprocess.config.RegistrationStepConfig attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) metric (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.workflows.preprocess.config.RegistrationStepConfig attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) min_event_level (thesis.core.output.modes.OutputConfig property) min_matches (thesis.core.path_declarations.GlobMatch attribute) min_patients (thesis.core.path_declarations.CohortPatients attribute) min_subjects (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) min_voxels (thesis.core.config.validators.ValidationConfig attribute) minimum_subjects (thesis.core.config.validators.HcpLooConfig attribute) mni_labels_list (thesis.workflows.preprocess.config.LabelTransformConfig attribute) mod_euler (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) mode (thesis.core.config.validators.SideThresholdConfig attribute) (thesis.core.output.modes.OutputConfig attribute) model (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) (thesis.workflows.preprocess.config.BedpostXConfig attribute) model_config (thesis.core.config.validators.AtlasConfig attribute) (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.core.config.validators.AtlasSourceConfig attribute) (thesis.core.config.validators.AtlasTransformConfig attribute) (thesis.core.config.validators.BaseConfig attribute) (thesis.core.config.validators.FireantsRegistrationConfig attribute) (thesis.core.config.validators.HardwareConfig attribute) (thesis.core.config.validators.HCPConfig attribute) (thesis.core.config.validators.HcpLooConfig attribute) (thesis.core.config.validators.NipypeConfig attribute) (thesis.core.config.validators.OutputSettingsConfig attribute) (thesis.core.config.validators.PathConfig attribute) (thesis.core.config.validators.PipelineConfig attribute) (thesis.core.config.validators.PreprocessingConfig attribute) (thesis.core.config.validators.QCConfig attribute) (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.core.config.validators.RegistrationViewerConfig attribute) (thesis.core.config.validators.S3Config attribute) (thesis.core.config.validators.SegmentationConfig attribute) (thesis.core.config.validators.SideThresholdConfig attribute) (thesis.core.config.validators.SynthSegConfig attribute) (thesis.core.config.validators.ThresholdGridConfig attribute) (thesis.core.config.validators.TractographyConfig attribute) (thesis.core.config.validators.TractSimilarityConfig attribute) (thesis.core.config.validators.TractSimilaritySweepConfig attribute) (thesis.core.config.validators.TransformJobConfig attribute) (thesis.core.config.validators.TransformsConfig attribute) (thesis.core.config.validators.ValidationConfig attribute) (thesis.core.output.modes.OutputConfig attribute) (thesis.core.output.summary.BatchSummary attribute) (thesis.core.output.summary.RunResult attribute) (thesis.core.output.summary.RunSummary attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasLossConfig attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasModelConfig attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasOptimizerConfig attribute) (thesis.workflows.preprocess.config.AcqParamsConfig attribute) (thesis.workflows.preprocess.config.BedpostXConfig attribute) (thesis.workflows.preprocess.config.BetConfig attribute) (thesis.workflows.preprocess.config.DTIFitConfig attribute) (thesis.workflows.preprocess.config.LabelTransformConfig attribute) (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) (thesis.workflows.preprocess.config.RegistrationChainConfig attribute) (thesis.workflows.preprocess.config.RegistrationStepConfig attribute) modify_bval() (in module thesis.workflows.preprocess.operations.file_ops) module thesis.cli thesis.core.config.loaders thesis.core.config.manager thesis.core.config.validators thesis.core.context thesis.core.contracts thesis.core.decorators thesis.core.exceptions thesis.core.gpu thesis.core.io thesis.core.logging thesis.core.logging.formatters thesis.core.logging.handlers thesis.core.nipype.executor thesis.core.nipype.interfaces.freesurfer thesis.core.nipype.interfaces.fsl thesis.core.output.events thesis.core.output.modes thesis.core.output.progress thesis.core.output.renderer thesis.core.output.summary thesis.core.path_declarations thesis.core.registry thesis.core.utils.utils thesis.workflows.atlas thesis.workflows.atlas._params thesis.workflows.atlas._statistics thesis.workflows.atlas.compute thesis.workflows.atlas.qc_metrics thesis.workflows.atlas.workflow thesis.workflows.atlas_to_patient.workflow thesis.workflows.full_pipeline._core thesis.workflows.full_pipeline.workflow thesis.workflows.hcp.config.params thesis.workflows.hcp.config.paths thesis.workflows.hcp.config.values thesis.workflows.hcp.nodes.roi thesis.workflows.hcp.nodes.roi_mapnode thesis.workflows.hcp.nodes.tractography thesis.workflows.hcp.operations.extraction thesis.workflows.hcp.operations.merging thesis.workflows.hcp.operations.resampling thesis.workflows.hcp.operations.streamline_warping thesis.workflows.hcp.operations.transformation thesis.workflows.hcp.operations.validation thesis.workflows.hcp.verifiers thesis.workflows.hcp.workflow thesis.workflows.learned_atlas thesis.workflows.learned_atlas._params thesis.workflows.learned_atlas.diagnostics thesis.workflows.learned_atlas.losses thesis.workflows.learned_atlas.model thesis.workflows.learned_atlas.train thesis.workflows.learned_atlas.workflow thesis.workflows.minimal thesis.workflows.mrtrix3.config.params thesis.workflows.mrtrix3.config.paths thesis.workflows.mrtrix3.config.values thesis.workflows.mrtrix3.nodes.fod thesis.workflows.mrtrix3.nodes.preprocessing thesis.workflows.mrtrix3.nodes.segmentation thesis.workflows.mrtrix3.nodes.tractography thesis.workflows.mrtrix3.operations.density_map thesis.workflows.mrtrix3.operations.mask_prep thesis.workflows.mrtrix3.operations.tckgen_adapter thesis.workflows.mrtrix3.workflow thesis.workflows.preprocess.config thesis.workflows.preprocess.nodes.diffusion thesis.workflows.preprocess.nodes.distortion thesis.workflows.preprocess.nodes.registration thesis.workflows.preprocess.nodes.structural thesis.workflows.preprocess.nodes.utils thesis.workflows.preprocess.operations.file_ops thesis.workflows.preprocess.operations.label_ops thesis.workflows.preprocess.workflow thesis.workflows.qc.checks thesis.workflows.qc.operations thesis.workflows.qc.roi_overlay thesis.workflows.qc.statistics thesis.workflows.qc.track_density thesis.workflows.qc.workflow thesis.workflows.registration.fireants_backend thesis.workflows.registration.paths thesis.workflows.registration.viewers thesis.workflows.registration.workflow thesis.workflows.synthseg.workflow thesis.workflows.tract_similarity._io thesis.workflows.tract_similarity._metrics thesis.workflows.tract_similarity.hcp_loo thesis.workflows.tract_similarity.sweep thesis.workflows.tract_similarity.workflow thesis.workflows.tract_synthseg.validation thesis.workflows.tract_synthseg.workflow thesis.workflows.transforms.operations thesis.workflows.transforms.workflow moments_moments (thesis.core.config.validators.FireantsRegistrationConfig attribute) moments_scale (thesis.core.config.validators.FireantsRegistrationConfig attribute) motion_correction (thesis.core.config.validators.PreprocessingConfig attribute) moving_image (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) moving_modality (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) mrtrix3 (thesis.core.config.validators.PipelineConfig attribute) MRTRIX3_ROI_OUTPUT_FIELDS (in module thesis.core.contracts) MRtrix3Params (class in thesis.workflows.mrtrix3.config.params) MRtrix3Paths (class in thesis.workflows.mrtrix3.config.paths) mtnormalise_node (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) N n_bins (thesis.core.config.validators.TractSimilarityConfig attribute) n_fibers (thesis.core.config.validators.HCPConfig attribute) n_fibres (thesis.workflows.preprocess.config.BedpostXConfig attribute) n_gpu_procs (thesis.core.config.validators.HardwareConfig attribute) n_gpus (thesis.core.config.validators.HardwareConfig attribute) n_jumps (thesis.workflows.preprocess.config.BedpostXConfig attribute) n_samples (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) n_steps (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) n_templates (thesis.workflows.learned_atlas._params.LearnedAtlasModelConfig attribute) name (thesis.core.config.validators.AtlasSourceConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.core.config.validators.TransformJobConfig attribute) (thesis.core.path_declarations.WorkingFile attribute) (thesis.core.registry.WorkflowEntry attribute) (thesis.workflows.full_pipeline._core.BackendDescriptor attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) next_step (thesis.core.output.summary.RunSummary attribute) nipype (thesis.core.config.validators.PipelineConfig attribute) NipypeConfig (class in thesis.core.config.validators) NipypeExecutor (class in thesis.core.nipype.executor) NipypeStatusCallback (class in thesis.core.nipype.executor) node_finished() (thesis.cli.ClickNodeProgress method) (thesis.core.output.progress.NodeProgressProtocol method) node_started() (thesis.cli.ClickNodeProgress method) (thesis.core.output.progress.NodeProgressProtocol method) NodeProgressProtocol (class in thesis.core.output.progress) NORMAL (thesis.core.output.modes.OutputMode attribute) normalization_method (thesis.core.config.validators.AtlasConfig attribute) (thesis.workflows.atlas._params.AtlasParams attribute) NormalizationMethod (class in thesis.core.config.validators) normalize (thesis.core.config.validators.FireantsRegistrationConfig attribute) O occupancy_entropy() (in module thesis.workflows.learned_atlas.diagnostics) OFF (thesis.core.output.modes.SummaryDetail attribute) opd (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) optimizer (thesis.core.config.validators.FireantsRegistrationConfig attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) optional (thesis.core.path_declarations.CohortPatients attribute) (thesis.core.path_declarations.ConfigList attribute) (thesis.core.path_declarations.DataDir attribute) (thesis.core.path_declarations.DataFile attribute) (thesis.core.path_declarations.ExternalFile attribute) (thesis.core.path_declarations.GlobGroup attribute) (thesis.core.path_declarations.GlobMatch attribute) (thesis.core.path_declarations.PatientDir attribute) (thesis.core.path_declarations.PatientFile attribute) (thesis.core.path_declarations.PriorOutput attribute) optional_patterns (thesis.core.config.validators.S3Config attribute) options (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) outlier_sd_threshold (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.core.config.validators.QCConfig attribute) output (thesis.core.config.validators.PipelineConfig attribute) output_dir (thesis.core.config.validators.PathConfig attribute) (thesis.core.context.ProcessingContext attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) output_format (thesis.core.config.validators.OutputSettingsConfig attribute) (thesis.core.output.modes.OutputConfig attribute) output_spec (thesis.core.nipype.interfaces.freesurfer.SynthSeg attribute) (thesis.core.nipype.interfaces.freesurfer.SynthStrip attribute) output_subdir (thesis.core.config.validators.AtlasConfig attribute) (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.TractSimilarityConfig attribute) (thesis.core.config.validators.TractSimilaritySweepConfig attribute) (thesis.core.config.validators.TransformJobConfig attribute) (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) OutputConfig (class in thesis.core.output.modes) OutputDir (class in thesis.core.path_declarations) OutputFormat (class in thesis.core.output.modes) OutputMode (class in thesis.core.output.modes) OutputRenderer (class in thesis.core.output.renderer) OutputSettingsConfig (class in thesis.core.config.validators) overlap_metrics() (in module thesis.workflows.tract_similarity._metrics) overlay_opacity (thesis.core.config.validators.RegistrationViewerConfig attribute) P padding (thesis.workflows.preprocess.config.BetConfig attribute) parc (thesis.core.config.validators.SynthSegConfig attribute) (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) parse_synthseg_qc_csv() (in module thesis.workflows.qc.checks) parse_synthseg_volumes_csv() (in module thesis.workflows.qc.checks) partial (thesis.core.output.summary.BatchSummary attribute) PARTIAL (thesis.core.output.summary.RunStatus attribute) PathConfig (class in thesis.core.config.validators) PathDeclaration (class in thesis.core.path_declarations) paths (thesis.core.config.validators.PipelineConfig attribute) patient_id (thesis.core.config.validators.PipelineConfig attribute) (thesis.core.context.ProcessingContext attribute) (thesis.core.output.events.Event attribute) (thesis.core.output.summary.RunResult attribute) (thesis.core.output.summary.RunSummary attribute) patient_to_template (thesis.core.config.validators.TransformsConfig attribute) PatientDir (class in thesis.core.path_declarations) PatientFile (class in thesis.core.path_declarations) pattern (thesis.core.path_declarations.GlobMatch attribute) phase0_go_no_go() (in module thesis.workflows.learned_atlas.diagnostics) phase_encoding_dirs (thesis.workflows.preprocess.config.AcqParamsConfig attribute) phsamples (thesis.workflows.hcp.config.paths.HCPPaths attribute) PipelineConfig (class in thesis.core.config.validators) PipelineError plugin (thesis.core.config.validators.NipypeConfig attribute) plugin_args (thesis.core.config.validators.NipypeConfig attribute) prefix (thesis.core.config.validators.S3Config attribute) prepare_5tt_node() (in module thesis.workflows.mrtrix3.nodes.segmentation) prepare_5tt_to_dwi_node() (in module thesis.workflows.mrtrix3.nodes.segmentation) prepare_ants_apply_transforms_node() (in module thesis.workflows.preprocess.nodes.registration) prepare_ants_registration_node() (in module thesis.workflows.preprocess.nodes.registration) prepare_atlas_extract_mapnode() (in module thesis.workflows.hcp.nodes.roi_mapnode) prepare_atlas_merge_joinnode() (in module thesis.workflows.hcp.nodes.roi_mapnode) prepare_atlas_transform_mapnode() (in module thesis.workflows.hcp.nodes.roi_mapnode) prepare_atlas_validate_mapnode() (in module thesis.workflows.hcp.nodes.roi_mapnode) prepare_bedpostx_node() (in module thesis.workflows.preprocess.nodes.diffusion) prepare_brain_extraction_node() (in module thesis.workflows.preprocess.nodes.distortion) prepare_brain_mask_task() (in module thesis.workflows.mrtrix3.operations.mask_prep) prepare_convert_to_short_node() (in module thesis.workflows.preprocess.nodes.distortion) prepare_create_index_node() (in module thesis.workflows.preprocess.nodes.utils) prepare_density_map_renamer() (in module thesis.workflows.mrtrix3.nodes.tractography) prepare_dtifit_node() (in module thesis.workflows.preprocess.nodes.diffusion) prepare_dwi2mask_node() (in module thesis.workflows.mrtrix3.nodes.preprocessing) prepare_dwi_import() (in module thesis.workflows.mrtrix3.nodes.preprocessing) prepare_eddy_node() (in module thesis.workflows.preprocess.nodes.distortion) prepare_extract_b0_node() (in module thesis.workflows.preprocess.nodes.distortion) prepare_final_merger() (in module thesis.workflows.hcp.nodes.roi_mapnode) prepare_fod_node() (in module thesis.workflows.mrtrix3.nodes.fod) prepare_gm_wm_csf_converter_node() (in module thesis.workflows.preprocess.nodes.structural) prepare_gmwmi_node() (in module thesis.workflows.mrtrix3.nodes.segmentation) prepare_hcp_paths() (in module thesis.workflows.hcp.config.paths) prepare_mask_node() (in module thesis.workflows.mrtrix3.nodes.preprocessing) prepare_merge_b0_node() (in module thesis.workflows.preprocess.nodes.distortion) prepare_modify_bval_node() (in module thesis.workflows.preprocess.nodes.utils) prepare_mrtrix3_params() (in module thesis.workflows.mrtrix3.config.params) prepare_mrtrix3_params_writer() (in module thesis.workflows.mrtrix3.nodes.tractography) prepare_mrtrix3_paths() (in module thesis.workflows.mrtrix3.config.paths) prepare_mtnormalise_node() (in module thesis.workflows.mrtrix3.nodes.fod) prepare_n4_bias_correction_node() (in module thesis.workflows.preprocess.nodes.structural) prepare_outdir_router() (in module thesis.workflows.hcp.nodes.tractography) prepare_per_target_maps_node() (in module thesis.workflows.mrtrix3.nodes.tractography) prepare_preprocess_paths() (in module thesis.workflows.preprocess.config) prepare_probtrackx2_node() (in module thesis.workflows.hcp.nodes.tractography) prepare_probtrackx2_outdir_router() (in module thesis.workflows.hcp.nodes.tractography) prepare_probtrackx2_params_writer() (in module thesis.workflows.hcp.nodes.tractography) prepare_response_node() (in module thesis.workflows.mrtrix3.nodes.fod) prepare_robust_fov_node() (in module thesis.workflows.preprocess.nodes.structural) prepare_roi_dwi_resampler() (in module thesis.workflows.hcp.nodes.roi) prepare_roi_validator() (in module thesis.workflows.hcp.nodes.roi) prepare_seed_path() (in module thesis.workflows.hcp.config.paths) prepare_streamline_warper() (in module thesis.workflows.hcp.nodes.tractography) prepare_synthseg_node() (in module thesis.workflows.preprocess.nodes.structural) prepare_synthseg_roi_extractor() (in module thesis.workflows.hcp.nodes.roi) prepare_synthseg_seg_resampler() (in module thesis.workflows.hcp.nodes.roi) prepare_tckgen_input_adapter() (in module thesis.workflows.mrtrix3.nodes.tractography) prepare_tckgen_node() (in module thesis.workflows.mrtrix3.nodes.tractography) prepare_tckmap_node() (in module thesis.workflows.mrtrix3.nodes.tractography) prepare_tcksift2_node() (in module thesis.workflows.mrtrix3.nodes.tractography) prepare_threshold_node() (in module thesis.workflows.preprocess.nodes.structural) prepare_topup_node() (in module thesis.workflows.preprocess.nodes.distortion) prepare_tract_masks_creator_node() (in module thesis.workflows.preprocess.nodes.structural) prepare_tractography_params() (in module thesis.workflows.hcp.config.params) prepare_waypoint_avoid_overlap_verifier() (in module thesis.workflows.hcp.nodes.roi) prepare_waytotal_writer() (in module thesis.workflows.mrtrix3.nodes.tractography) preprocess (thesis.core.config.validators.PipelineConfig attribute) preprocess_wf (thesis.workflows.full_pipeline._core.CoreScaffold attribute) PreprocessConfig (class in thesis.workflows.preprocess.config) preprocessing (thesis.core.config.validators.PipelineConfig attribute) PreprocessingConfig (class in thesis.core.config.validators) PreprocessPaths (class in thesis.workflows.preprocess.config) PreprocessSynthSegConfig (class in thesis.workflows.preprocess.config) presence_value (thesis.core.config.validators.AtlasConfig attribute) (thesis.workflows.atlas._params.AtlasParams attribute) presence_weight (thesis.workflows.learned_atlas._params.LearnedAtlasLossConfig attribute) present_gpu_binaries() (in module thesis.core.gpu) primary_dir (thesis.core.path_declarations.GlobGroup attribute) (thesis.core.path_declarations.GlobMatch attribute) PriorOutput (class in thesis.core.path_declarations) ProbTrackX2 (class in thesis.core.nipype.interfaces.fsl) ProbTrackX2GPU (class in thesis.core.nipype.interfaces.fsl) probtrackx_relpath (thesis.core.config.validators.TractSimilarityConfig attribute) ProcessingContext (class in thesis.core.context) ProcessingError produces() (in module thesis.core.decorators) progress (thesis.core.config.validators.OutputSettingsConfig attribute) (thesis.core.output.modes.OutputConfig attribute) protocol (thesis.core.config.validators.PipelineConfig attribute) Q qc (thesis.core.config.validators.PipelineConfig attribute) (thesis.core.config.validators.SynthSegConfig attribute) (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) qc_subdir (thesis.workflows.atlas.compute.QcParams attribute) QCConfig (class in thesis.core.config.validators) QcParams (class in thesis.workflows.atlas.compute) QUIET (thesis.core.output.modes.OutputMode attribute) R radius (thesis.workflows.preprocess.config.BetConfig attribute) rand_fib (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) read_sift2_mu() (in module thesis.workflows.mrtrix3.operations.density_map) reason (thesis.core.gpu.GPUStatus attribute) recursive (thesis.core.path_declarations.PriorOutput attribute) recursive_fallback (thesis.core.path_declarations.GlobGroup attribute) (thesis.core.path_declarations.GlobMatch attribute) reference_image (thesis.core.config.validators.AtlasTransformConfig attribute) (thesis.core.config.validators.TransformJobConfig attribute) (thesis.core.config.validators.TransformsConfig attribute) reg_method (thesis.workflows.full_pipeline._core.CoreScaffold attribute) region (thesis.core.config.validators.S3Config attribute) register() (thesis.core.registry.WorkflowRegistry method) registration (thesis.core.config.validators.PipelineConfig attribute) (thesis.workflows.preprocess.config.PreprocessConfig attribute) registration_transform_filenames() (in module thesis.workflows.registration.paths) registration_wf (thesis.workflows.full_pipeline._core.CoreScaffold attribute) RegistrationChainConfig (class in thesis.workflows.preprocess.config) RegistrationConfig (class in thesis.core.config.validators) RegistrationError RegistrationJobConfig (class in thesis.core.config.validators) RegistrationStepConfig (class in thesis.workflows.preprocess.config) RegistrationViewerConfig (class in thesis.core.config.validators) regression_to_mean_control() (in module thesis.workflows.learned_atlas.diagnostics) remove_unnecessary_outputs (thesis.core.config.validators.NipypeConfig attribute) rename_density_map_task() (in module thesis.workflows.mrtrix3.operations.density_map) render_batch_summary() (thesis.core.output.renderer.OutputRenderer method) render_event() (thesis.core.output.renderer.OutputRenderer method) render_run_summary() (thesis.core.output.renderer.OutputRenderer method) required_binaries (thesis.workflows.full_pipeline._core.BackendDescriptor attribute) required_patterns (thesis.core.config.validators.S3Config attribute) requires() (in module thesis.core.decorators) resample_label_map_task() (in module thesis.workflows.hcp.operations.resampling) resample_rois_to_dwi_task() (in module thesis.workflows.hcp.operations.resampling) reset_event_bus() (in module thesis.core.output.events) reset_logging() (in module thesis.core.logging) residual_variance_map() (in module thesis.workflows.learned_atlas.diagnostics) resolve() (thesis.core.path_declarations.CohortDir method) (thesis.core.path_declarations.CohortPatients method) (thesis.core.path_declarations.ConfigList method) (thesis.core.path_declarations.DataDir method) (thesis.core.path_declarations.DataFile method) (thesis.core.path_declarations.ExternalFile method) (thesis.core.path_declarations.GlobGroup method) (thesis.core.path_declarations.GlobMatch method) (thesis.core.path_declarations.OutputDir method) (thesis.core.path_declarations.PathDeclaration method) (thesis.core.path_declarations.PatientDir method) (thesis.core.path_declarations.PatientFile method) (thesis.core.path_declarations.PriorOutput method) (thesis.core.path_declarations.WorkingFile method) resolve_atlas_file() (in module thesis.workflows.tract_similarity._io) resolve_background_image() (in module thesis.workflows.qc.operations) resolve_fixed_image() (in module thesis.workflows.registration.paths) resolve_fixed_image_for_job() (in module thesis.workflows.registration.paths) resolve_hcp_value() (in module thesis.workflows.hcp.config.values) resolve_moving_image() (in module thesis.workflows.registration.paths) resolve_moving_image_for_job() (in module thesis.workflows.registration.paths) resolve_mrtrix3_value() (in module thesis.workflows.mrtrix3.config.values) resolve_path() (in module thesis.core.utils.utils) resolve_registration_jobs() (in module thesis.workflows.registration.paths) resolve_t1_for_synthseg() (in module thesis.workflows.synthseg.workflow) ResolvedRegistrationJob (class in thesis.workflows.registration.paths) response_algorithm (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) response_node (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) result (thesis.core.output.summary.RunSummary attribute) results (thesis.core.context.ProcessingContext attribute) retries (thesis.core.output.summary.BatchSummary attribute) retry_backoff (thesis.core.config.validators.S3Config attribute) retry_count (thesis.core.output.summary.RunResult attribute) rigid_iterations (thesis.core.config.validators.FireantsRegistrationConfig attribute) rigid_lr (thesis.core.config.validators.FireantsRegistrationConfig attribute) robust (thesis.core.config.validators.SynthSegConfig attribute) (thesis.workflows.preprocess.config.BetConfig attribute) (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) roi_file (thesis.core.config.validators.AtlasSourceConfig attribute) roi_files (thesis.core.config.validators.TractographyConfig attribute) roi_labels (thesis.core.config.validators.TractographyConfig attribute) ROI_OUTPUT_FIELDS (in module thesis.core.contracts) root_dir (thesis.core.path_declarations.CohortPatients attribute) run_bedpostx (thesis.workflows.full_pipeline._core.BackendDescriptor attribute) (thesis.workflows.preprocess.config.PreprocessConfig attribute) run_coregistration (thesis.workflows.preprocess.config.PreprocessConfig attribute) run_dtifit (thesis.workflows.preprocess.config.PreprocessConfig attribute) run_eddy (thesis.workflows.preprocess.config.PreprocessConfig attribute) run_fireants_cli_task() (in module thesis.workflows.registration.fireants_backend) run_fireants_registration_task() (in module thesis.workflows.registration.fireants_backend) run_on_t1 (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) run_on_t2 (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) run_post_workflow_qc() (in module thesis.workflows.qc.operations) run_qc_for_patient() (in module thesis.workflows.qc.operations) run_robustfov (thesis.workflows.preprocess.config.PreprocessConfig attribute) run_summaries (thesis.core.output.summary.BatchSummary attribute) run_synthseg (thesis.workflows.preprocess.config.PreprocessConfig attribute) run_tcksift2_task() (in module thesis.workflows.mrtrix3.operations.density_map) run_topup (thesis.workflows.preprocess.config.PreprocessConfig attribute) run_tractography (thesis.core.config.validators.TractographyConfig attribute) run_workflow() (in module thesis.core.nipype.executor) RunResult (class in thesis.core.output.summary) RunStatus (class in thesis.core.output.summary) RunSummary (class in thesis.core.output.summary) S s3 (thesis.core.config.validators.PipelineConfig attribute) S3Config (class in thesis.core.config.validators) safe_name (thesis.workflows.registration.paths.ResolvedRegistrationJob property) sample_every (thesis.workflows.preprocess.config.BedpostXConfig attribute) samples_base_name (thesis.workflows.hcp.config.paths.HCPPaths attribute) save_bvals() (in module thesis.core.io) save_bvecs() (in module thesis.core.io) save_config() (thesis.core.config.manager.ConfigManager method) save_fields (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) save_nifti() (in module thesis.core.io) save_tensor (thesis.workflows.preprocess.config.DTIFitConfig attribute) save_yaml() (in module thesis.core.config.loaders) scales (thesis.core.config.validators.FireantsRegistrationConfig attribute) scratch_dir (thesis.core.config.validators.PathConfig attribute) scripts_dir (thesis.core.config.validators.PathConfig attribute) seed (thesis.workflows.learned_atlas._params.LearnedAtlasOptimizerConfig attribute) seed_roi (thesis.core.config.validators.TractographyConfig attribute) seed_strategy (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) segmentation (thesis.core.config.validators.PipelineConfig attribute) SegmentationConfig (class in thesis.core.config.validators) SegmentationError select_backend() (in module thesis.workflows.full_pipeline._core) set_console_level() (in module thesis.core.logging) setup_logging() (in module thesis.core.logging) SharedSubgraph (class in thesis.workflows.mrtrix3.workflow) show_progress (thesis.core.output.modes.OutputConfig property) SideThresholdConfig (class in thesis.core.config.validators) similarity_weight (thesis.workflows.learned_atlas._params.LearnedAtlasLossConfig attribute) singularity_threshold (thesis.core.config.validators.ValidationConfig attribute) skipped (thesis.core.output.summary.BatchSummary attribute) SKIPPED (thesis.core.output.summary.RunStatus attribute) slurm (thesis.core.config.validators.PipelineConfig attribute) smoothness_weight (thesis.workflows.learned_atlas._params.LearnedAtlasLossConfig attribute) SOFTMAX (thesis.core.config.validators.NormalizationMethod attribute) start (thesis.core.config.validators.ThresholdGridConfig attribute) start() (thesis.cli.ClickNodeProgress method) (thesis.core.output.progress.NodeProgressProtocol method) status (thesis.core.output.summary.RunResult attribute) (thesis.core.output.summary.RunSummary attribute) step (thesis.core.config.validators.ThresholdGridConfig attribute) step_length (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.hcp.config.params.TractographyParams attribute) steps_completed (thesis.core.output.summary.RunResult attribute) steps_failed (thesis.core.output.summary.RunResult attribute) stop (thesis.core.config.validators.ThresholdGridConfig attribute) stop() (thesis.cli.ClickNodeProgress method) (thesis.core.output.progress.NodeProgressProtocol method) stop_on_first_crash (thesis.core.config.validators.NipypeConfig attribute) str_fields (thesis.core.path_declarations.ConfigList attribute) STREAMLINE_DENSITY (thesis.core.config.validators.NormalizationMethod attribute) subdir (thesis.core.path_declarations.CohortDir attribute) (thesis.core.path_declarations.CohortPatients attribute) (thesis.core.path_declarations.OutputDir attribute) (thesis.core.path_declarations.PriorOutput attribute) subject_density_threshold (thesis.core.config.validators.AtlasQCConfig attribute) (thesis.workflows.atlas.compute.QcParams attribute) subject_threshold (thesis.core.config.validators.TractSimilarityConfig attribute) subject_threshold_grid (thesis.core.config.validators.TractSimilaritySweepConfig attribute) subscribe() (thesis.core.output.events.EventBus method) succeeded (thesis.core.output.summary.BatchSummary attribute) SUCCESS (thesis.core.output.summary.RunStatus attribute) suggested_follow_up (thesis.core.output.summary.BatchSummary attribute) suggested_next_step (thesis.core.output.summary.RunResult attribute) summarize_dice_scores() (in module thesis.workflows.atlas.qc_metrics) summary (thesis.core.config.validators.OutputSettingsConfig attribute) (thesis.core.output.modes.OutputConfig attribute) SummaryDetail (class in thesis.core.output.modes) suppress_nipype_native_logging() (in module thesis.core.logging) suspend_console_logging() (in module thesis.core.logging) SynthSeg (class in thesis.core.nipype.interfaces.freesurfer) synthseg (thesis.core.config.validators.PipelineConfig attribute) (thesis.workflows.preprocess.config.PreprocessConfig attribute) synthseg_qc_threshold (thesis.core.config.validators.QCConfig attribute) synthseg_roi_labels (thesis.core.config.validators.TractographyConfig attribute) SynthSegConfig (class in thesis.core.config.validators) SynthStrip (class in thesis.core.nipype.interfaces.freesurfer) T t1_final (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) t1_image (thesis.core.config.validators.HCPConfig attribute) (thesis.core.config.validators.SynthSegConfig attribute) (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) t1_path (thesis.workflows.hcp.config.paths.HCPPaths attribute) (thesis.workflows.mrtrix3.config.paths.MRtrix3Paths attribute) t1_to_template (thesis.workflows.preprocess.config.RegistrationChainConfig attribute) t2_final (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) t2_image (thesis.core.config.validators.HCPConfig attribute) (thesis.workflows.preprocess.config.PreprocessConfig attribute) (thesis.workflows.preprocess.config.PreprocessPaths attribute) t2_to_t1 (thesis.workflows.preprocess.config.RegistrationChainConfig attribute) tckgen_algorithm (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) tckgen_backtrack (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) tckgen_crop_at_gmwmi (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) tckgen_cutoff (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) tckgen_maxlength (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) tckgen_minlength (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) tckgen_seeds (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) tckgen_select (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) template_reference_image (thesis.core.config.validators.TransformsConfig attribute) template_to_patient (thesis.core.config.validators.AtlasTransformConfig attribute) (thesis.core.config.validators.TransformsConfig attribute) thesis.cli module thesis.core.config.loaders module thesis.core.config.manager module thesis.core.config.validators module thesis.core.context module thesis.core.contracts module thesis.core.decorators module thesis.core.exceptions module thesis.core.gpu module thesis.core.io module thesis.core.logging module thesis.core.logging.formatters module thesis.core.logging.handlers module thesis.core.nipype.executor module thesis.core.nipype.interfaces.freesurfer module thesis.core.nipype.interfaces.fsl module thesis.core.output.events module thesis.core.output.modes module thesis.core.output.progress module thesis.core.output.renderer module thesis.core.output.summary module thesis.core.path_declarations module thesis.core.registry module thesis.core.utils.utils module thesis.workflows.atlas module thesis.workflows.atlas._params module thesis.workflows.atlas._statistics module thesis.workflows.atlas.compute module thesis.workflows.atlas.qc_metrics module thesis.workflows.atlas.workflow module thesis.workflows.atlas_to_patient.workflow module thesis.workflows.full_pipeline._core module thesis.workflows.full_pipeline.workflow module thesis.workflows.hcp.config.params module thesis.workflows.hcp.config.paths module thesis.workflows.hcp.config.values module thesis.workflows.hcp.nodes.roi module thesis.workflows.hcp.nodes.roi_mapnode module thesis.workflows.hcp.nodes.tractography module thesis.workflows.hcp.operations.extraction module thesis.workflows.hcp.operations.merging module thesis.workflows.hcp.operations.resampling module thesis.workflows.hcp.operations.streamline_warping module thesis.workflows.hcp.operations.transformation module thesis.workflows.hcp.operations.validation module thesis.workflows.hcp.verifiers module thesis.workflows.hcp.workflow module thesis.workflows.learned_atlas module thesis.workflows.learned_atlas._params module thesis.workflows.learned_atlas.diagnostics module thesis.workflows.learned_atlas.losses module thesis.workflows.learned_atlas.model module thesis.workflows.learned_atlas.train module thesis.workflows.learned_atlas.workflow module thesis.workflows.minimal module thesis.workflows.mrtrix3.config.params module thesis.workflows.mrtrix3.config.paths module thesis.workflows.mrtrix3.config.values module thesis.workflows.mrtrix3.nodes.fod module thesis.workflows.mrtrix3.nodes.preprocessing module thesis.workflows.mrtrix3.nodes.segmentation module thesis.workflows.mrtrix3.nodes.tractography module thesis.workflows.mrtrix3.operations.density_map module thesis.workflows.mrtrix3.operations.mask_prep module thesis.workflows.mrtrix3.operations.tckgen_adapter module thesis.workflows.mrtrix3.workflow module thesis.workflows.preprocess.config module thesis.workflows.preprocess.nodes.diffusion module thesis.workflows.preprocess.nodes.distortion module thesis.workflows.preprocess.nodes.registration module thesis.workflows.preprocess.nodes.structural module thesis.workflows.preprocess.nodes.utils module thesis.workflows.preprocess.operations.file_ops module thesis.workflows.preprocess.operations.label_ops module thesis.workflows.preprocess.workflow module thesis.workflows.qc.checks module thesis.workflows.qc.operations module thesis.workflows.qc.roi_overlay module thesis.workflows.qc.statistics module thesis.workflows.qc.track_density module thesis.workflows.qc.workflow module thesis.workflows.registration.fireants_backend module thesis.workflows.registration.paths module thesis.workflows.registration.viewers module thesis.workflows.registration.workflow module thesis.workflows.synthseg.workflow module thesis.workflows.tract_similarity._io module thesis.workflows.tract_similarity._metrics module thesis.workflows.tract_similarity.hcp_loo module thesis.workflows.tract_similarity.sweep module thesis.workflows.tract_similarity.workflow module thesis.workflows.tract_synthseg.validation module thesis.workflows.tract_synthseg.workflow module thesis.workflows.transforms.operations module thesis.workflows.transforms.workflow module ThesisError threads (thesis.core.config.validators.HardwareConfig attribute) (thesis.core.config.validators.SynthSegConfig attribute) (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) threshold_core_mask() (in module thesis.workflows.atlas.qc_metrics) ThresholdGridConfig (class in thesis.core.config.validators) thsamples (thesis.workflows.hcp.config.paths.HCPPaths attribute) timestamp (thesis.core.output.events.Event attribute) tissue_types (thesis.core.config.validators.SegmentationConfig attribute) to_dict() (thesis.core.config.validators.PipelineConfig method) (thesis.core.context.ProcessingContext method) to_path() (in module thesis.core.utils.utils) topup (thesis.core.config.validators.PreprocessingConfig attribute) total (thesis.core.output.summary.BatchSummary attribute) total_elapsed_seconds (thesis.core.output.summary.BatchSummary attribute) track_density_thresholds (thesis.core.config.validators.QCConfig attribute) tract_similarity (thesis.core.config.validators.PipelineConfig attribute) tract_similarity_sweep (thesis.core.config.validators.PipelineConfig attribute) tract_similarity_wf (thesis.workflows.full_pipeline._core.CoreScaffold attribute) tractography (thesis.core.config.validators.PipelineConfig attribute) tractography_edges (thesis.workflows.full_pipeline._core.BackendDescriptor attribute) tractography_relpath (thesis.core.config.validators.AtlasConfig attribute) TractographyConfig (class in thesis.core.config.validators) TractographyError TractographyParams (class in thesis.workflows.hcp.config.params) TractSimilarityConfig (class in thesis.core.config.validators) TractSimilaritySweepConfig (class in thesis.core.config.validators) train_learned_atlas() (in module thesis.workflows.learned_atlas.train) training_space (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) transform (thesis.core.config.validators.AtlasSourceConfig attribute) transform_mni_labels (thesis.workflows.preprocess.config.LabelTransformConfig attribute) transform_rois_task() (in module thesis.workflows.hcp.operations.transformation) transform_type (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.workflows.preprocess.config.RegistrationStepConfig attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) TransformJobConfig (class in thesis.core.config.validators) transforms (thesis.core.config.validators.PipelineConfig attribute) TransformsConfig (class in thesis.core.config.validators) true_support_mask() (in module thesis.workflows.learned_atlas.diagnostics) U unsubscribe() (thesis.core.output.events.EventBus method) use_float (thesis.core.config.validators.RegistrationConfig attribute) (thesis.core.config.validators.RegistrationJobConfig attribute) (thesis.workflows.preprocess.config.RegistrationStepConfig attribute) (thesis.workflows.registration.paths.ResolvedRegistrationJob attribute) use_gpu (thesis.workflows.preprocess.config.BedpostXConfig attribute) use_hcp_template (thesis.workflows.preprocess.config.LabelTransformConfig attribute) use_inverse_warp (thesis.workflows.preprocess.config.LabelTransformConfig attribute) use_mtnormalise (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) use_profiler (thesis.core.config.validators.NipypeConfig attribute) use_sift2 (thesis.core.config.validators.TractographyConfig attribute) (thesis.workflows.mrtrix3.config.params.MRtrix3Params attribute) use_waypoints (thesis.core.config.validators.TractographyConfig attribute) use_wls (thesis.workflows.preprocess.config.DTIFitConfig attribute) V validate_backend() (thesis.core.config.validators.RegistrationViewerConfig class method) validate_bet_method() (thesis.core.config.validators.PreprocessingConfig class method) validate_cache_policy() (thesis.core.config.validators.S3Config class method) validate_deform_algo() (thesis.core.config.validators.FireantsRegistrationConfig class method) validate_deformation_type() (thesis.core.config.validators.FireantsRegistrationConfig class method) validate_direction() (thesis.core.config.validators.TransformJobConfig class method) validate_driver() (thesis.core.config.validators.FireantsRegistrationConfig class method) validate_dtype() (thesis.core.config.validators.FireantsRegistrationConfig class method) validate_fivett_algorithm() (thesis.core.config.validators.TractographyConfig class method) validate_fod_algorithm() (thesis.core.config.validators.TractographyConfig class method) validate_hemisphere() (thesis.core.config.validators.TractographyConfig class method) validate_interpolation() (thesis.core.config.validators.RegistrationJobConfig class method) (thesis.core.config.validators.TransformJobConfig class method) validate_inverse_method() (thesis.core.config.validators.FireantsRegistrationConfig class method) validate_loss_type() (thesis.core.config.validators.FireantsRegistrationConfig class method) validate_mask_source() (thesis.core.config.validators.TractographyConfig class method) validate_method() (thesis.core.config.validators.RegistrationConfig class method) (thesis.core.config.validators.RegistrationJobConfig class method) (thesis.core.config.validators.SegmentationConfig class method) (thesis.core.config.validators.TractographyConfig class method) (thesis.workflows.preprocess.config.RegistrationStepConfig class method) validate_moving_modality() (thesis.core.config.validators.RegistrationConfig class method) (thesis.core.config.validators.RegistrationJobConfig class method) validate_optimizer() (thesis.core.config.validators.FireantsRegistrationConfig class method) validate_output_format() (thesis.core.config.validators.OutputSettingsConfig class method) validate_plugin() (thesis.core.config.validators.NipypeConfig class method) validate_progress() (thesis.core.config.validators.OutputSettingsConfig class method) validate_response_algorithm() (thesis.core.config.validators.TractographyConfig class method) validate_scale_lengths() (thesis.core.config.validators.FireantsRegistrationConfig method) validate_seed_strategy() (thesis.core.config.validators.TractographyConfig class method) validate_summary() (thesis.core.config.validators.OutputSettingsConfig class method) validate_thresholds() (thesis.core.config.validators.QCConfig class method) validate_transform_inputs() (in module thesis.workflows.transforms.operations) validate_transform_type() (thesis.core.config.validators.RegistrationConfig class method) (thesis.core.config.validators.RegistrationJobConfig class method) (thesis.workflows.preprocess.config.RegistrationStepConfig class method) validate_verbosity() (thesis.core.config.validators.OutputSettingsConfig class method) validate_warped_rois_passthrough_task() (in module thesis.workflows.hcp.operations.validation) validate_warped_rois_task() (in module thesis.workflows.hcp.operations.validation) validate_waypoints_file() (in module thesis.workflows.qc.checks) validation (thesis.core.config.validators.PipelineConfig attribute) ValidationConfig (class in thesis.core.config.validators) ValidationError value (thesis.core.config.validators.SideThresholdConfig attribute) values (thesis.core.config.validators.ThresholdGridConfig attribute) VERBOSE (thesis.core.output.modes.OutputMode attribute) verbosity (thesis.core.config.validators.OutputSettingsConfig attribute) verifier (thesis.core.registry.WorkflowEntry attribute) verify() (in module thesis.core.decorators) verify_cohort_requirements() (in module thesis.workflows.tract_similarity.workflow) verify_jacobian (thesis.workflows.learned_atlas._params.LearnedAtlasConfig attribute) verify_requirements() (in module thesis.workflows.atlas.workflow) (in module thesis.workflows.atlas_to_patient.workflow) (in module thesis.workflows.full_pipeline.workflow) (in module thesis.workflows.hcp.verifiers) (in module thesis.workflows.learned_atlas.workflow) (in module thesis.workflows.preprocess.workflow) (in module thesis.workflows.qc.workflow) (in module thesis.workflows.registration.workflow) (in module thesis.workflows.tract_similarity.hcp_loo) (in module thesis.workflows.tract_similarity.workflow) (in module thesis.workflows.tract_synthseg.workflow) (in module thesis.workflows.transforms.workflow) verify_sweep_requirements() (in module thesis.workflows.tract_similarity.sweep) verify_waypoint_avoid_overlap_task() (in module thesis.workflows.hcp.operations.validation) viewer (thesis.core.config.validators.RegistrationConfig attribute) vol (thesis.core.config.validators.SynthSegConfig attribute) (thesis.workflows.preprocess.config.PreprocessSynthSegConfig attribute) volume_ratio_max (thesis.core.config.validators.ValidationConfig attribute) volume_ratio_min (thesis.core.config.validators.ValidationConfig attribute) voxel_size_mm() (in module thesis.workflows.tract_similarity._io) W warn_unprefixed_gpu_runtime_env() (thesis.core.config.validators.TractographyConfig class method) WARNING (thesis.core.output.events.EventLevel attribute) warnings (thesis.core.output.summary.RunResult attribute) waypoint_files (thesis.core.config.validators.TractographyConfig attribute) waypoint_labels (thesis.core.config.validators.AtlasSourceConfig attribute) waypoint_masks (thesis.core.config.validators.TractographyConfig attribute) WAYTOTAL (thesis.core.config.validators.NormalizationMethod attribute) waytotal_name (thesis.core.config.validators.TractSimilarityConfig attribute) weight (thesis.workflows.preprocess.config.BedpostXConfig attribute) wire_core_scaffold() (in module thesis.workflows.full_pipeline._core) wm_fod_field (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) wm_fod_owner (thesis.workflows.mrtrix3.workflow.SharedSubgraph attribute) workflow (thesis.core.output.summary.BatchSummary attribute) (thesis.core.output.summary.RunResult attribute) (thesis.core.output.summary.RunSummary attribute) workflow() (in module thesis.core.decorators) WorkflowEntry (class in thesis.core.registry) WorkflowRegistry (class in thesis.core.registry) working_dir (thesis.core.config.validators.NipypeConfig attribute) (thesis.core.context.ProcessingContext attribute) WorkingFile (class in thesis.core.path_declarations) write_composite_transform (thesis.core.config.validators.RegistrationConfig attribute) (thesis.workflows.preprocess.config.RegistrationStepConfig attribute) write_list_file() (in module thesis.core.utils.utils) write_volumes (thesis.core.config.validators.HcpLooConfig attribute) write_waytotal_task() (in module thesis.workflows.mrtrix3.operations.density_map)
