Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z _ __init__() (CPAC.network_centrality.utils.MethodOptionError method) (CPAC.network_centrality.utils.ThresholdError method) (CPAC.network_centrality.utils.ThresholdOptionError method) (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.pipeline.nipype_pipeline_engine.Workflow method) (CPAC.utils.interfaces.function.Function method) (CPAC.utils.monitoring.custom_logging.MockLogger method) (nipype.interfaces.base.core.Interface method) (nipype.utils.logger.Logging method) A add_afni_prefix() (in module CPAC.utils.utils) add_nodes() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) affine_file_from_params_file() (in module CPAC.generate_motion_statistics) affine_from_params() (in module CPAC.generate_motion_statistics) aggregate_outputs() (CPAC.utils.interfaces.function.Function method) (nipype.interfaces.base.core.Interface method) alff_falff() (in module CPAC.alff.alff) alff_falff_space_template() (in module CPAC.alff.alff) all_native_filter (CPAC.utils.outputs.Outputs attribute) all_template_filter (CPAC.utils.outputs.Outputs attribute) always_run (CPAC.utils.interfaces.function.Function property) (nipype.interfaces.base.core.Interface property) anat (CPAC.utils.outputs.Outputs attribute) anat_based_mask() (in module CPAC.func_preproc.func_preproc) anat_refined_mask() (in module CPAC.func_preproc.func_preproc) any (CPAC.utils.outputs.Outputs attribute) append_name() (CPAC.utils.strategy.Strategy method) as_matrix() (CPAC.utils.ndmg_utils.graph method) B bandpass_voxels() (in module CPAC.nuisance) base_dir (CPAC.pipeline.nipype_pipeline_engine.MapNode attribute) (CPAC.pipeline.nipype_pipeline_engine.Node attribute) (CPAC.pipeline.nipype_pipeline_engine.Workflow attribute) bids_decode_fname() (in module CPAC.utils.bids_utils) bids_entities_from_filename() (in module CPAC.utils.bids_utils) bids_gen_cpac_sublist() (in module CPAC.utils.bids_utils) bids_match_entities() (in module CPAC.utils.bids_utils) bids_parse_sidecar() (in module CPAC.utils.bids_utils) bids_remove_entity() (in module CPAC.utils.bids_utils) bids_retrieve_params() (in module CPAC.utils.bids_utils) bids_shortest_entity() (in module CPAC.utils.bids_utils) bidsier_prefix() (in module CPAC.utils.datasource) bold_mask_afni() (in module CPAC.func_preproc.func_preproc) bold_mask_anatomical_based() (in module CPAC.func_preproc.func_preproc) bold_mask_anatomical_refined() (in module CPAC.func_preproc.func_preproc) bold_mask_anatomical_resampled() (in module CPAC.func_preproc.func_preproc) bold_mask_ccs() (in module CPAC.func_preproc.func_preproc) bold_mask_fsl() (in module CPAC.func_preproc.func_preproc) bold_mask_fsl_afni() (in module CPAC.func_preproc.func_preproc) bold_masking() (in module CPAC.func_preproc.func_preproc) bold_ts (CPAC.utils.outputs.Outputs attribute) C calc_delta_te_and_asym_ratio() (in module CPAC.utils.datasource) calc_motion_stats() (in module CPAC.func_preproc.func_motion) calculate_DVARS() (in module CPAC.generate_motion_statistics) calculate_FD_J() (in module CPAC.generate_motion_statistics) calculate_FD_P() (in module CPAC.generate_motion_statistics) calculate_resource_timeseries() (in module CPAC.utils.monitoring.draw_gantt_chart) camelCase() (in module CPAC.utils.bids_utils) can_resume (CPAC.utils.interfaces.function.Function property) (nipype.interfaces.base.core.Interface property) check() (in module CPAC.utils.utils) check_centrality_params() (in module CPAC.network_centrality.utils) check_command_path() (in module CPAC.utils.utils) check_config_resources() (in module CPAC.utils.utils) check_for_s3() (in module CPAC.utils.datasource) check_func_scan() (in module CPAC.utils.datasource) check_if_file_is_empty() (in module CPAC.seg_preproc) check_multicollinearity() (in module CPAC.utils.create_fsl_model) check_pattern() (CPAC.utils.configuration.Configuration method) check_pname() (in module CPAC.utils.configuration) check_prov_for_motion_tool() (in module CPAC.utils.utils) check_prov_for_regtool() (in module CPAC.utils.utils) check_random_state() (in module CPAC.utils.utils) check_system_deps() (in module CPAC.utils.utils) check_tr() (in module CPAC.utils.utils) chunk_ts() (in module CPAC.func_preproc.utils) ciftis (CPAC.utils.outputs.Outputs attribute) cl_strip_brackets() (in module CPAC.utils.bids_utils) clone() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.pipeline.nipype_pipeline_engine.Workflow method) collect_arguments() (in module CPAC.func_preproc.func_preproc) collect_bids_files_configs() (in module CPAC.utils.bids_utils) combine_multiple_entity_instances() (in module CPAC.utils.bids_utils) compile_strategy_name() (in module CPAC.utils.symlinks) compute_datasink_dirs() (in module CPAC.utils.trimmer) compute_fisher_z_score() (in module CPAC.sca) (in module CPAC.utils.utils) compute_reho() (in module CPAC.reho) concat_list() (in module CPAC.utils.utils) concordance() (in module CPAC.utils.test_init) Configuration (class in CPAC.utils.configuration) (class in CPAC.utils.extract_data) (class in CPAC.utils.extract_data_multiscan) configuration_strategy_mock() (in module CPAC.utils.test_mocks) connect() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) connect_centrality_workflow() (in module CPAC.network_centrality.pipeline) connect_func_ingress() (in module CPAC.func_preproc.func_ingress) convert_pvalue_to_r() (in module CPAC.network_centrality.utils) copy_geom() (in module CPAC.easy_thresh) cor_graph() (CPAC.utils.ndmg_utils.graph method) correlation() (in module CPAC.utils.utils) cosine_filter() (in module CPAC.nuisance) CPAC.alff module CPAC.alff.alff module CPAC.alff.utils module CPAC.cwas module CPAC.easy_thresh module CPAC.func_preproc.func_ingress module CPAC.func_preproc.func_motion module CPAC.func_preproc.func_preproc module CPAC.func_preproc.utils module CPAC.generate_motion_statistics module CPAC.group_analysis module CPAC.isc module CPAC.network_centrality.network_centrality module CPAC.network_centrality.pipeline module CPAC.network_centrality.utils module CPAC.nuisance module CPAC.pipeline.schema module, [1] CPAC.pipeline.utils module CPAC.qc.xcp module CPAC.registration module CPAC.reho module CPAC.sca module CPAC.scrubbing module CPAC.seg_preproc module CPAC.timeseries module CPAC.utils.bids_utils module CPAC.utils.configuration module CPAC.utils.create_flame_model_files module CPAC.utils.create_fsl_flame_preset module CPAC.utils.create_fsl_model module CPAC.utils.create_group_analysis_info_files module CPAC.utils.datasource module CPAC.utils.datatypes module CPAC.utils.docs module CPAC.utils.extract_data module CPAC.utils.extract_data_multiscan module CPAC.utils.extract_parameters module CPAC.utils.ga module CPAC.utils.interfaces.function module CPAC.utils.interfaces.tests module CPAC.utils.misc module CPAC.utils.monitoring module CPAC.utils.monitoring.draw_gantt_chart module CPAC.utils.ndmg_utils module CPAC.utils.nifti_utils module CPAC.utils.outputs module CPAC.utils.pytest module CPAC.utils.strategy module CPAC.utils.symlinks module CPAC.utils.test_init module CPAC.utils.test_mocks module CPAC.utils.test_resources module CPAC.utils.tests module CPAC.utils.trimmer module CPAC.utils.typing module CPAC.utils.utils module CPAC.utils.versioning module CPAC.vmhc module create_alff() (in module CPAC.alff.alff) create_anat_datasource() (in module CPAC.utils.datasource) create_bbregister_func_to_anat() (in module CPAC.registration) create_centrality_wf() (in module CPAC.network_centrality.network_centrality) create_check_for_s3_node() (in module CPAC.utils.datasource) create_con_file() (in module CPAC.utils.create_flame_model_files) (in module CPAC.utils.create_fsl_model) create_con_ftst_file() (in module CPAC.utils.create_flame_model_files) (in module CPAC.utils.create_fsl_model) create_contrasts_template_df() (in module CPAC.utils.create_fsl_flame_preset) create_cpac_data_config() (in module CPAC.utils.bids_utils) create_cwas() (in module CPAC.cwas) create_design_matrix() (in module CPAC.utils.create_fsl_model) create_design_matrix_df() (in module CPAC.utils.create_fsl_flame_preset) create_dummy_node() (in module CPAC.utils.test_init) create_dummy_string() (in module CPAC.utils.create_flame_model_files) (in module CPAC.utils.create_fsl_model) create_event_dict() (in module CPAC.utils.monitoring.draw_gantt_chart) create_flame_model_files() (in module CPAC.utils.create_flame_model_files) create_fmap_datasource() (in module CPAC.utils.datasource) create_fsl_flame_wf() (in module CPAC.group_analysis) create_fsl_fnirt_nonlinear_reg() (in module CPAC.registration) create_fsl_fnirt_nonlinear_reg_nhp() (in module CPAC.registration) create_fts_file() (in module CPAC.utils.create_flame_model_files) (in module CPAC.utils.create_fsl_model) create_func_datasource() (in module CPAC.utils.datasource) create_general_datasource() (in module CPAC.utils.datasource) create_grp_analysis_dataflow() (in module CPAC.utils.datasource) create_grp_file() (in module CPAC.utils.create_flame_model_files) (in module CPAC.utils.create_fsl_model) create_id_string() (in module CPAC.utils.utils) create_log() (in module CPAC.utils.utils) create_merge_node() (in module CPAC.network_centrality.utils) create_output_mean_csv() (in module CPAC.utils.utils) create_paths_to_symlinks() (in module CPAC.utils.symlinks) create_pheno_dict() (in module CPAC.utils.create_fsl_model) create_register_func_to_anat() (in module CPAC.registration) create_register_func_to_anat_use_T2() (in module CPAC.registration) create_regressor_workflow() (in module CPAC.nuisance) create_reho() (in module CPAC.reho) create_roi_mask_dataflow() (in module CPAC.utils.datasource) create_sca() (in module CPAC.sca) create_scale_func_wf() (in module CPAC.func_preproc.func_preproc) create_scrubbing_preproc() (in module CPAC.scrubbing) create_seg_preproc_antsJointLabel_method() (in module CPAC.seg_preproc) create_spatial_map_dataflow() (in module CPAC.utils.datasource) create_symlinks() (in module CPAC.utils.symlinks) create_temporal_reg() (in module CPAC.sca) create_wf_calculate_ants_warp() (in module CPAC.registration) create_wf_edit_func() (in module CPAC.func_preproc.func_preproc) critical() (CPAC.utils.monitoring.custom_logging.MockLogger method) D debug() (CPAC.utils.monitoring.custom_logging.MockLogger method) debugging (CPAC.utils.outputs.Outputs attribute) default_bucket_name() (in module CPAC.utils.test_init) degrees_to_mm() (in module CPAC.func_preproc.utils) delete() (CPAC.utils.monitoring.custom_logging.MockLogger method) delete_nested_value() (in module CPAC.utils.utils) DICT (in module CPAC.utils.typing) dict() (CPAC.utils.configuration.Configuration method) disconnect() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) do_it() (in module CPAC.utils.ga) docstring_parameter() (in module CPAC.utils.docs) download_cpac_resources_from_s3() (in module CPAC.utils.test_init) download_resource_from_s3() (in module CPAC.utils.test_init) draw_nodes() (in module CPAC.utils.monitoring.draw_gantt_chart) dvcorr() (in module CPAC.qc.xcp) E easy_thresh() (in module CPAC.easy_thresh) erosion() (in module CPAC.seg_preproc) error() (CPAC.utils.monitoring.custom_logging.MockLogger method) estimate_reference_image() (in module CPAC.func_preproc.func_motion) exception() (CPAC.utils.monitoring.custom_logging.MockLogger method) expand_workflow() (in module CPAC.utils.trimmer) export() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) extract_data() (in module CPAC.utils.extract_data) (in module CPAC.utils.extract_data_multiscan) extract_one_d() (in module CPAC.utils.utils) extract_output_mean() (in module CPAC.utils.utils) extract_scan_params_dct() (in module CPAC.utils.datasource) extract_txt() (in module CPAC.utils.utils) F f_kendall() (in module CPAC.reho) failed_to_start() (in module CPAC.utils.monitoring) file_node() (in module CPAC.utils.test_mocks) find_files() (in module CPAC.utils.utils) find_offending_time_points() (in module CPAC.nuisance) fork() (CPAC.utils.strategy.Strategy method) fullname (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) (CPAC.pipeline.nipype_pipeline_engine.Workflow property) func (CPAC.utils.outputs.Outputs attribute) func_despike() (in module CPAC.func_preproc.func_preproc) func_despike_template() (in module CPAC.func_preproc.func_preproc) func_mask_normalize() (in module CPAC.func_preproc.func_preproc) func_mean() (in module CPAC.func_preproc.func_preproc) func_motion_correct() (in module CPAC.func_preproc.func_motion) func_motion_correct_only() (in module CPAC.func_preproc.func_motion) func_motion_estimates() (in module CPAC.func_preproc.func_motion) func_normalize() (in module CPAC.func_preproc.func_preproc) func_reorient() (in module CPAC.func_preproc.func_preproc) func_scaling() (in module CPAC.func_preproc.func_preproc) func_slice_time() (in module CPAC.func_preproc.func_preproc) func_truncate() (in module CPAC.func_preproc.func_preproc) Function (class in CPAC.utils.interfaces.function), [1] functional_timeseries (CPAC.utils.outputs.Outputs attribute) G gather_echo_times() (in module CPAC.utils.datasource) gather_extraction_maps() (in module CPAC.utils.datasource) gen_bids_outputs_sublist() (in module CPAC.utils.bids_utils) gen_motion_parameters() (in module CPAC.generate_motion_statistics) gen_power_parameters() (in module CPAC.generate_motion_statistics) gen_roi_timeseries() (in module CPAC.timeseries) gen_vertices_timeseries() (in module CPAC.timeseries) gen_voxel_timeseries() (in module CPAC.timeseries) generate_gantt_chart() (in module CPAC.utils.monitoring.draw_gantt_chart) generate_summarize_tissue_mask() (in module CPAC.nuisance) generate_suplimentary_files() (in module CPAC.utils.extract_data_multiscan) generate_supplementary_files() (in module CPAC.utils.extract_data) generate_xcp_qc() (in module CPAC.qc.xcp) get() (CPAC.utils.strategy.Strategy method) get_bids_info() (in module CPAC.qc.xcp) get_custom_roi_info() (in module CPAC.utils.create_fsl_model) get_fisher_zscore() (in module CPAC.utils.utils) get_flag() (in module CPAC.utils.utils) get_flag_wf() (in module CPAC.utils.utils) get_fmap_phasediff_metadata() (in module CPAC.utils.datasource) get_forking_labels() (CPAC.utils.strategy.Strategy static method) get_forking_points() (CPAC.utils.strategy.Strategy static method) get_graph() (CPAC.utils.ndmg_utils.graph method) get_highest_local_res() (in module CPAC.utils.datasource) get_idx() (in module CPAC.func_preproc.func_preproc) get_img_nvols() (in module CPAC.vmhc) get_indx() (in module CPAC.scrubbing) get_last_prov_entry() (in module CPAC.utils.utils) get_leaf_properties() (CPAC.utils.strategy.Strategy method) get_map() (in module CPAC.utils.datasource) get_mcflirt_rms_abs() (in module CPAC.func_preproc.func_motion) get_measure_dict() (in module CPAC.utils.create_fsl_model) get_motion_ref() (in module CPAC.func_preproc.func_motion) get_mov_parameters() (in module CPAC.scrubbing) get_name() (CPAC.utils.strategy.Strategy method) get_nested() (CPAC.utils.configuration.Configuration method) get_node() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) get_node_from_resource_pool() (CPAC.utils.strategy.Strategy method) get_nodes_names() (CPAC.utils.strategy.Strategy method) get_operand_expression() (in module CPAC.vmhc) get_operand_string() (in module CPAC.utils.utils) get_operation() (in module CPAC.group_analysis) get_opt_string() (in module CPAC.alff.utils) get_or_create_config() (in module CPAC.utils.ga) get_output() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) get_resource_pool() (CPAC.utils.strategy.Strategy method) get_rest() (in module CPAC.utils.datasource) get_roi_num_list() (in module CPAC.utils.utils) get_roi_timeseries() (in module CPAC.timeseries) get_scan_params() (in module CPAC.utils.utils) get_spatial_map_timeseries() (in module CPAC.timeseries) get_standard_background_img() (in module CPAC.easy_thresh) get_subnodes() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) get_template_specs() (in module CPAC.utils.misc) get_tr() (in module CPAC.utils.utils) get_tuple() (in module CPAC.easy_thresh) get_uid() (in module CPAC.utils.ga) get_vertices_timeseries() (in module CPAC.timeseries) get_voxel_timeseries() (in module CPAC.timeseries) get_zscore() (in module CPAC.utils.utils) getLogger() (in module CPAC.utils.monitoring) (in module CPAC.utils.monitoring.custom_logging) (in module logging) (nipype.utils.logger.Logging method) getOpString() (in module CPAC.reho) giftis (CPAC.utils.outputs.Outputs attribute) grab() (in module CPAC.utils.extract_parameters) graph (class in CPAC.utils.ndmg_utils) greater_than() (in module CPAC.utils.create_fsl_model) group_files_in_strategies() (in module CPAC.utils.symlinks) H handle() (CPAC.utils.monitoring.LoggingRequestHandler method) hardcoded_antsJointLabelFusion() (in module CPAC.seg_preproc) hash_exists() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) help() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.utils.interfaces.function.Function class method) (nipype.interfaces.base.core.Interface class method) I ImageTo1D (class in CPAC.generate_motion_statistics) info() (CPAC.utils.monitoring.custom_logging.MockLogger method) ingress_func_metadata() (in module CPAC.utils.datasource) input_spec (CPAC.generate_motion_statistics.ImageTo1D attribute) (CPAC.utils.interfaces.function.Function attribute), [1] (nipype.interfaces.base.core.Interface attribute) inputs (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) insert_entity() (in module CPAC.utils.bids_utils) Interface (class in nipype.interfaces.base.core) interface (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) inverse_nifti_values() (in module CPAC.utils.nifti_utils) is_cached() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) is_datasink() (in module CPAC.utils.trimmer) ItemFromList (class in CPAC.utils.datatypes) ITERABLE (in module CPAC.utils.typing) itername (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) (CPAC.pipeline.nipype_pipeline_engine.Workflow property) J joint_mask() (in module CPAC.cwas) K key_type_error() (CPAC.utils.configuration.Configuration method) keys() (CPAC.utils.configuration.Configuration method) L LIST (in module CPAC.utils.typing) list_files() (in module CPAC.utils.trimmer) list_item_replace() (in module CPAC.utils.utils) list_node_names() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) ListFromItem (class in CPAC.utils.datatypes) load() (CPAC.pipeline.nipype_pipeline_engine.MapNode static method) (CPAC.pipeline.nipype_pipeline_engine.Node static method) (CPAC.pipeline.nipype_pipeline_engine.Workflow static method) load_cpac_data_config() (in module CPAC.utils.bids_utils) load_group_participant_list() (in module CPAC.utils.create_fsl_model) load_inputs_from_json() (CPAC.utils.interfaces.function.Function method) load_pheno_file() (in module CPAC.utils.create_fsl_model) load_yaml_config() (in module CPAC.utils.bids_utils) log_nodes_cb() (in module CPAC.utils.monitoring), [1] log_nodes_initial() (in module CPAC.utils.monitoring) log_subprocess() (in module CPAC.utils.monitoring.custom_logging) LoggingHTTPServer (class in CPAC.utils.monitoring) LoggingRequestHandler (class in CPAC.utils.monitoring) lookup_nested_value() (in module CPAC.utils.utils) M make_graph() (CPAC.utils.ndmg_utils.graph method) map_to_roi() (in module CPAC.sca) MapNode (class in CPAC.pipeline.nipype_pipeline_engine) mask_erosion() (in module CPAC.seg_preproc) match_epi_fmaps() (in module CPAC.utils.datasource) mem_gb (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) mem_x (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) merge() (in module CPAC.utils.extract_parameters) merge_lists() (in module CPAC.network_centrality.utils) MethodOptionError mm_to_degrees() (in module CPAC.func_preproc.utils) MockLogger (class in CPAC.utils.monitoring.custom_logging) model_group_var_separately() (in module CPAC.utils.create_fsl_model) module CPAC.alff CPAC.alff.alff CPAC.alff.utils CPAC.cwas CPAC.easy_thresh CPAC.func_preproc.func_ingress CPAC.func_preproc.func_motion CPAC.func_preproc.func_preproc CPAC.func_preproc.utils CPAC.generate_motion_statistics CPAC.group_analysis CPAC.isc CPAC.network_centrality.network_centrality CPAC.network_centrality.pipeline CPAC.network_centrality.utils CPAC.nuisance CPAC.pipeline.schema, [1] CPAC.pipeline.utils CPAC.qc.xcp CPAC.registration CPAC.reho CPAC.sca CPAC.scrubbing CPAC.seg_preproc CPAC.timeseries CPAC.utils.bids_utils CPAC.utils.configuration CPAC.utils.create_flame_model_files CPAC.utils.create_fsl_flame_preset CPAC.utils.create_fsl_model CPAC.utils.create_group_analysis_info_files CPAC.utils.datasource CPAC.utils.datatypes CPAC.utils.docs CPAC.utils.extract_data CPAC.utils.extract_data_multiscan CPAC.utils.extract_parameters CPAC.utils.ga CPAC.utils.interfaces.function CPAC.utils.interfaces.tests CPAC.utils.misc CPAC.utils.monitoring CPAC.utils.monitoring.draw_gantt_chart CPAC.utils.ndmg_utils CPAC.utils.nifti_utils CPAC.utils.outputs CPAC.utils.pytest CPAC.utils.strategy CPAC.utils.symlinks CPAC.utils.test_init CPAC.utils.test_mocks CPAC.utils.test_resources CPAC.utils.tests CPAC.utils.trimmer CPAC.utils.typing CPAC.utils.utils CPAC.utils.versioning CPAC.vmhc monitor_server() (in module CPAC.utils.monitoring) more_zeros_than_ones() (in module CPAC.utils.nifti_utils) motion_correct_3dvolreg() (in module CPAC.func_preproc.func_motion) motion_correct_connections() (in module CPAC.func_preproc.func_motion) motion_correct_mcflirt() (in module CPAC.func_preproc.func_motion) motion_estimate_filter() (in module CPAC.func_preproc.func_motion) motion_power_statistics() (in module CPAC.generate_motion_statistics) N n_procs (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) name (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) (CPAC.pipeline.nipype_pipeline_engine.Workflow property) name_fork() (in module CPAC.pipeline.utils) name_motion_filter() (in module CPAC.pipeline.schema), [1] native_nonsmooth (CPAC.utils.outputs.Outputs attribute) native_raw (CPAC.utils.outputs.Outputs attribute) native_smooth (CPAC.utils.outputs.Outputs attribute) ndmg_create_graphs() (in module CPAC.utils.ndmg_utils) ndmg_roi_timeseries() (in module CPAC.utils.ndmg_utils) negative() (in module CPAC.utils.create_fsl_model) network_centrality() (in module CPAC.network_centrality.pipeline) nifti_cwas() (in module CPAC.cwas) nifti_image_input() (in module CPAC.utils.nifti_utils) Node (class in CPAC.pipeline.nipype_pipeline_engine) normalize_motion_parameters() (in module CPAC.func_preproc.func_motion) notch_filter_motion() (in module CPAC.func_preproc.utils) nullify() (in module CPAC.func_preproc.utils) num_subnodes() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) O oned_text_concat() (in module CPAC.func_preproc.utils) ordereddict_to_dict() (in module CPAC.utils.utils) output_dir() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) output_spec (CPAC.generate_motion_statistics.ImageTo1D attribute) (CPAC.utils.interfaces.function.Function attribute), [1] (nipype.interfaces.base.core.Interface attribute) Outputs (class in CPAC.utils.outputs) outputs (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) override_mem_gb() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) P pearson_correlation() (in module CPAC.utils.test_init) permutation_message() (in module CPAC.pipeline.schema), [1] pick_tissue_from_labels_file_interface() (in module CPAC.utils.interfaces.function) pick_wm() (in module CPAC.utils.utils) pick_wm_class_0() (in module CPAC.seg_preproc) pick_wm_class_1() (in module CPAC.seg_preproc) pick_wm_class_2() (in module CPAC.seg_preproc) pick_wm_prob_0() (in module CPAC.seg_preproc) pick_wm_prob_1() (in module CPAC.seg_preproc) pick_wm_prob_2() (in module CPAC.seg_preproc) populate_all_templates() (in module CPAC.utils.test_init) populate_template_config() (in module CPAC.utils.test_init) positive() (in module CPAC.utils.create_fsl_model) preconfig_yaml() (in module CPAC.utils.configuration) Preconfiguration (class in CPAC.utils.configuration) present_outputs() (in module CPAC.pipeline.utils) preset_paired_two_group() (in module CPAC.utils.create_fsl_flame_preset) preset_single_group_avg() (in module CPAC.utils.create_fsl_flame_preset) preset_tripled_two_group() (in module CPAC.utils.create_fsl_flame_preset) preset_unpaired_two_group() (in module CPAC.utils.create_fsl_flame_preset) process_contrast() (in module CPAC.utils.create_fsl_model) process_pheno_file() (in module CPAC.utils.create_fsl_model) process_segment_map() (in module CPAC.seg_preproc) Q qc_xcp() (in module CPAC.qc.xcp) R random_seed_flags() (in module CPAC.pipeline.random_state.seed) read_csv() (in module CPAC.utils.extract_data) (in module CPAC.utils.extract_data_multiscan) read_group_list_text_file() (in module CPAC.utils.create_fsl_flame_preset) read_json() (in module CPAC.utils.utils) read_pheno_csv_into_df() (in module CPAC.utils.create_fsl_flame_preset) recurse_nodes() (in module CPAC.utils.monitoring) reference (CPAC.utils.outputs.Outputs attribute) reference_csv (CPAC.utils.outputs.Outputs attribute) remove_False() (in module CPAC.utils.utils) remove_nodes() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) remove_None() (in module CPAC.utils.utils) repickle() (in module CPAC.utils.utils) replace_in_strings() (in module CPAC.utils.utils) res_in_filename() (in module CPAC.utils.bids_utils) res_string_to_tuple() (in module CPAC.utils.datasource) resample_func_roi() (in module CPAC.utils.datasource) resolve_resolution() (in module CPAC.utils.datasource) resource_overusage_report() (in module CPAC.utils.monitoring.draw_gantt_chart) resource_pool (CPAC.utils.strategy.Strategy property) resource_report() (in module CPAC.utils.monitoring.draw_gantt_chart) result (CPAC.pipeline.nipype_pipeline_engine.MapNode property) (CPAC.pipeline.nipype_pipeline_engine.Node property) return_all_niis() (in module CPAC.utils.test_init) return_aws_creds() (in module CPAC.utils.test_init) return_config_elements() (CPAC.utils.configuration.Configuration method) return_resource_dir() (in module CPAC.utils.test_init) return_resource_subfolder() (in module CPAC.utils.test_init) return_strats_obj() (in module CPAC.utils.test_init) return_subj_measure_dirs() (in module CPAC.utils.test_init) return_subject_list() (in module CPAC.utils.test_init) return_test_subj() (in module CPAC.utils.test_init) rpool (CPAC.utils.strategy.Strategy property) run() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.pipeline.nipype_pipeline_engine.Workflow method) (CPAC.utils.interfaces.function.Function method) (in module CPAC.utils.create_fsl_flame_preset) (in module CPAC.utils.create_fsl_model) (in module CPAC.utils.extract_data) (in module CPAC.utils.extract_data_multiscan) (in module CPAC.utils.extract_parameters) (nipype.interfaces.base.core.Interface method) S safe_shape() (in module CPAC.utils.utils) sanitize() (in module CPAC.pipeline.schema), [1] save() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.pipeline.nipype_pipeline_engine.Workflow method) save_graph() (CPAC.utils.ndmg_utils.graph method) save_inputs_to_json() (CPAC.utils.interfaces.function.Function method) schema() (in module CPAC.pipeline.schema), [1] select_model_files() (in module CPAC.utils.datasource) sep_nifti_subbriks() (in module CPAC.network_centrality.utils) set_from_ENV() (CPAC.utils.configuration.Configuration method) set_input() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) set_leaf_properties() (CPAC.utils.strategy.Strategy method) set_nested() (CPAC.utils.configuration.Configuration method) set_nested_value() (in module CPAC.utils.utils) set_subject() (in module CPAC.utils.configuration) set_up_logger() (in module CPAC.utils.monitoring) set_without_ENV() (CPAC.utils.configuration.Configuration method) setup_test_logger() (in module CPAC.utils.test_init) setup_test_wf() (in module CPAC.utils.test_resources) sig_imports() (CPAC.utils.interfaces.function.Function static method), [1] skipif() (in module CPAC.utils.pytest) slice_timing_wf() (in module CPAC.func_preproc.func_preproc) smooth_nii_file() (in module CPAC.utils.test_init) source_set() (in module CPAC.pipeline.utils) split_ts_chunks() (in module CPAC.func_preproc.utils) str_to_bool1_1() (in module CPAC.pipeline.schema), [1] Strategy (class in CPAC.utils.strategy) sub_list_filter_by_labels() (in module CPAC.utils.bids_utils) sub_pattern() (CPAC.utils.configuration.Configuration method) summary() (CPAC.utils.ndmg_utils.graph method) switch_is_off() (CPAC.utils.configuration.Configuration method) switch_is_on() (CPAC.utils.configuration.Configuration method) switch_is_on_off() (CPAC.utils.configuration.Configuration method) T template_nonsmooth (CPAC.utils.outputs.Outputs attribute) template_raw (CPAC.utils.outputs.Outputs attribute) template_smooth (CPAC.utils.outputs.Outputs attribute) the_trimmer() (in module CPAC.utils.trimmer) ThresholdError ThresholdOptionError to_fisherz (CPAC.utils.outputs.Outputs attribute) to_smooth (CPAC.utils.outputs.Outputs attribute) to_zstd (CPAC.utils.outputs.Outputs attribute) track_config() (in module CPAC.utils.ga) track_event() (in module CPAC.utils.ga) track_run() (in module CPAC.utils.ga) try_fetch_parameter() (in module CPAC.utils.utils) TUPLE (in module CPAC.utils.typing) U update() (CPAC.pipeline.nipype_pipeline_engine.MapNode method) (CPAC.pipeline.nipype_pipeline_engine.Node method) (CPAC.utils.configuration.Configuration method) update_config_dict() (in module CPAC.utils.utils) update_nested_dict() (in module CPAC.utils.utils) update_pipeline_values_1_8() (in module CPAC.utils.utils) update_resource_pool() (CPAC.utils.strategy.Strategy method) update_values_from_list() (in module CPAC.utils.utils) V version (CPAC.utils.interfaces.function.Function property) (nipype.interfaces.base.core.Interface property) version_report() (in module CPAC.utils.docs) W warning() (CPAC.utils.monitoring.custom_logging.MockLogger method) with_key() (in module CPAC.utils.bids_utils) without_key() (in module CPAC.utils.bids_utils) Workflow (class in CPAC.pipeline.nipype_pipeline_engine) write_blank_contrast_csv() (in module CPAC.utils.create_group_analysis_info_files) write_config_dct_to_yaml() (in module CPAC.utils.create_fsl_flame_preset) write_custom_readme_file() (in module CPAC.utils.create_group_analysis_info_files) write_dataframe_to_csv() (in module CPAC.utils.create_fsl_flame_preset) write_design_matrix_csv() (in module CPAC.utils.create_group_analysis_info_files) write_graph() (CPAC.pipeline.nipype_pipeline_engine.Workflow method) write_group_list_text_file() (in module CPAC.utils.create_fsl_flame_preset) write_mat_file() (in module CPAC.utils.create_flame_model_files) (in module CPAC.utils.create_fsl_model) write_output_json() (in module CPAC.utils.utils) write_to_log() (in module CPAC.utils.utils) Z zscore() (in module CPAC.utils.utils)