Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W _ __add__() (petpal.pipelines.steps_containers.StepsContainer method) __call__() (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase method) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF method) (petpal.io.image.ImageLoader method) (petpal.kinetic_modeling.graphical_analysis.GraphicalAnalysis method) (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis method) (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) (petpal.kinetic_modeling.parametric_images.ReferenceTissueParametricImage method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTACFitter method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis method) (petpal.kinetic_modeling.tac_uncertainty.TacUncertainty method) (petpal.meta.auto_cli.ParseKwargs method) (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) (petpal.pipelines.steps_base.StepsAPI method) (petpal.pipelines.steps_containers.StepsContainer method) (petpal.pipelines.steps_containers.StepsPipeline method) (petpal.preproc.decay_correction.DecayFix method) (petpal.preproc.motion_corr.MotionCorrect method) (petpal.preproc.motion_target.MotionTarget method) (petpal.preproc.regional_tac_extraction.WriteRegionalTacs method) (petpal.preproc.register.RegisterPet method) (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm method) (petpal.utils.metadata.BidsMetadataMender method) __getitem__() (petpal.pipelines.steps_containers.StepsContainer method) __len__() (petpal.utils.time_activity_curve.TimeActivityCurve method) __post_init__() (petpal.utils.time_activity_curve.TimeActivityCurve method) __repr__() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.pipelines.BIDSyPathsForPipelines method) (petpal.pipelines.pipelines.BIDSyPathsForRawData method) (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) (petpal.pipelines.steps_containers.StepsContainer method) (petpal.pipelines.steps_containers.StepsPipeline method) __str__() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.pipelines.BIDSyPathsForPipelines method) (petpal.pipelines.pipelines.BIDSyPathsForRawData method) (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.ArgsDict method) (petpal.pipelines.steps_base.FunctionBasedStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) (petpal.pipelines.steps_containers.StepsContainer method) (petpal.pipelines.steps_containers.StepsPipeline method) _add_decay_factors() (petpal.utils.metadata.BidsMetadataMender method) _add_empty_decay_factors() (petpal.utils.metadata.BidsMetadataMender method) _add_frame_reference_times() (petpal.utils.metadata.BidsMetadataMender method) _add_frame_times_start() (petpal.utils.metadata.BidsMetadataMender method) _add_half_life() (petpal.utils.metadata.BidsMetadataMender method) _add_missing_keys() (petpal.utils.metadata.BidsMetadataMender method) _atomic_save() (petpal.io.table.TableSaver method) _calc_frtm_or_srtm_fit_props() (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis method) _calc_mrtm_fit_props() (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis method) _CONV_TCM_MODELS_CONFIGS (in module petpal.kinetic_modeling.tac_fitting) _EXAMPLE_ (in module petpal.cli.cli_tac_fitting) _FRAME_AVGD_TCM_CONFIGS (in module petpal.kinetic_modeling.tac_fitting) _generate_formatted_bounds() (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis method) _generate_pretty_bounds() (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis method) _generate_pretty_params() (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis method) _generate_quantile_params() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter static method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase static method) _get_kwargs() (petpal.meta.auto_cli.ParseKwargs method) _get_pretty_frtm_fit_param_vals() (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis static method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis static method) _get_pretty_srtm_fit_param_vals() (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis static method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis static method) _get_tcm_function() (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis static method) _linear_function() (petpal.input_function.blood_input.BloodInputFunction static method) _noise_term_func() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter static method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase static method) _peak_term_func() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter static method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase static method) _PIB_EXAMPLE_ (in module petpal.cli.cli_pib_processing) _PLOT_EXAMPLES_ (in module petpal.cli.cli_plot_tacs) _PREPROC_EXAMPLES_ (in module petpal.cli.cli_preproc) _pull_image_if_not_exists() (petpal.preproc.partial_volume_corrections.PetPvc method) _RTM_EXAMPLES_ (in module petpal.cli.cli_reference_tissue_models) _save_fit_props() (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) _save_multifitprops_table() (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) _save_multitacs_table() (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) _select_fig_class_based_on_method() (petpal.visualizations.graphical_plots.Plot static method) _setup_bounds() (petpal.kinetic_modeling.tac_fitting.FrameAveragedTACFitter method) (petpal.kinetic_modeling.tac_fitting.TACFitter method) (petpal.kinetic_modeling.tac_fitting.TACFitterWithoutBloodVolume method) _setup_weights() (petpal.kinetic_modeling.tac_fitting.FrameAveragedTACFitter method) _smoothness_term_func() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter static method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase static method) _TEXT_BOX_ (in module petpal.utils.testing_utils) _to_file() (petpal.utils.metadata.BidsMetadataMender method) _validate_directory() (petpal.visualizations.graphical_plots.Plot static method) _validate_filepath() (petpal.visualizations.graphical_plots.Plot static method) _validate_inputs() (petpal.kinetic_modeling.tac_fitting.FrameAveragedTACFitter method) (petpal.kinetic_modeling.tac_fitting.TACFitter method) (petpal.kinetic_modeling.tac_fitting.TACFitterWithoutBloodVolume method) _validate_view() (petpal.visualizations.image_visualization.NiftiGifCreator method) _VAT_EXAMPLE_ (in module petpal.cli.cli_vat_processing) _voxel_term_func() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter static method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase static method) A add_container() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) add_data_plots() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) add_dependency() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) add_errorbar() (petpal.visualizations.tac_plots.RegionalTacFigure method) (petpal.visualizations.tac_plots.TacFigure method) add_figure_axes_labels_and_legend() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) add_fit_lines() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) add_fit_points() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) add_plots() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) add_shading_plots() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) add_step() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsContainer method) (petpal.pipelines.steps_containers.StepsPipeline method) add_tac() (petpal.visualizations.tac_plots.RegionalTacFigure method) (petpal.visualizations.tac_plots.TacFigure method) add_zero_time_and_activity() (petpal.utils.time_activity_curve.TimeActivityCurve method) affine_parse() (petpal.utils.image_io.ImageIO static method) all_args_non_empty_strings() (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) all_call_kwargs_non_empty_strings() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) all_init_kwargs_non_empty_strings() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) all_kwargs_non_empty_strings() (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) alpha (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep property) anat_path (petpal.pipelines.pipelines.BIDS_Pipeline property) (petpal.pipelines.pipelines.BIDSyPathsForPipelines property) (petpal.pipelines.pipelines.BIDSyPathsForRawData property) ants_xfm_to_rigid_pars() (petpal.preproc.motion_corr.MotionCorrect static method) apply_factor() (petpal.preproc.decay_correction.DecayCorrect method) (petpal.preproc.decay_correction.DecayFix method) apply_motion_correction() (petpal.preproc.motion_corr.MotionCorrect method) apply_transform() (petpal.preproc.register.RegisterPet method) B beta (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep property) bids_dir (petpal.pipelines.pipelines.BIDS_Pipeline property) (petpal.pipelines.pipelines.BIDSyPathsForPipelines property) (petpal.pipelines.pipelines.BIDSyPathsForRawData property) blood_path (petpal.pipelines.pipelines.BIDS_Pipeline property) (petpal.pipelines.pipelines.BIDSyPathsForPipelines property) (petpal.pipelines.pipelines.BIDSyPathsForRawData property) built-in function petpal.cli.cli_graphical_analysis._add_common_args() petpal.cli.cli_preproc._add_common_args() petpal.cli.cli_preproc._generate_args() petpal.cli.cli_pvc.sgtm_cli_run() petpal.cli.cli_reference_tissue_models._generate_bounds() petpal.cli.cli_reference_tissue_models._pretty_print_results() petpal.cli.cli_reference_tissue_models.add_common_args() petpal.cli.cli_reference_tissue_models.parse_args() petpal.cli.cli_tac_fitting._generate_args() petpal.cli.cli_tac_fitting._generate_bounds() petpal.cli.cli_tac_fitting.add_common_analysis_args() petpal.cli.cli_tac_fitting.add_common_io_args() petpal.cli.cli_tac_fitting.add_common_print_args() petpal.cli.cli_tac_fitting.fit_props_printer() petpal.cli.cli_tac_interpolation._print_tac_to_screen() petpal.cli.cli_tac_interpolation._safe_write_tac() petpal.cli.cli_vat_processing.infer_group() petpal.cli.cli_vat_processing.rename_subs() petpal.cli.cli_vat_processing.vat_protocol() petpal.input_function.blood_input.extract_blood_input_function_activity_from_csv() petpal.input_function.blood_input.extract_blood_input_function_from_csv() petpal.input_function.blood_input.extract_blood_input_function_times_from_csv() petpal.input_function.blood_input.read_plasma_glucose_concentration() petpal.input_function.blood_input.resample_blood_data_on_scanner_times() petpal.input_function.idif_necktangle.average_across_4d_frames() petpal.input_function.idif_necktangle.double_threshold_idif_from_4d_pet_necktangle() petpal.input_function.idif_necktangle.get_frame_time_midpoints() petpal.input_function.idif_necktangle.load_fslmeants_to_numpy_3d() petpal.input_function.idif_necktangle.single_threshold_idif_from_4d_pet_with_necktangle() petpal.io.table.get_tabular_separator() petpal.kinetic_modeling.fit_tac_with_rtms.get_rtm_kwargs() petpal.kinetic_modeling.fit_tac_with_rtms.get_rtm_method() petpal.kinetic_modeling.fit_tac_with_rtms.get_rtm_output_size() petpal.kinetic_modeling.graphical_analysis._line_fitting_make_rhs_matrix_from_xdata() petpal.kinetic_modeling.graphical_analysis.alternative_logan_analysis() petpal.kinetic_modeling.graphical_analysis.alternative_logan_analysis_with_rsquared() petpal.kinetic_modeling.graphical_analysis.calculate_patlak_x() petpal.kinetic_modeling.graphical_analysis.cumulative_trapezoidal_integral() petpal.kinetic_modeling.graphical_analysis.fit_line_to_data_using_lls() petpal.kinetic_modeling.graphical_analysis.fit_line_to_data_using_lls_with_rsquared() petpal.kinetic_modeling.graphical_analysis.get_graphical_analysis_method() petpal.kinetic_modeling.graphical_analysis.get_graphical_analysis_method_with_rsquared() petpal.kinetic_modeling.graphical_analysis.get_index_from_threshold() petpal.kinetic_modeling.graphical_analysis.km_multifit_analysis_to_jsons() petpal.kinetic_modeling.graphical_analysis.km_multifit_analysis_to_tsv() petpal.kinetic_modeling.graphical_analysis.linear_least_squares_fit_with_stats() petpal.kinetic_modeling.graphical_analysis.logan_analysis() petpal.kinetic_modeling.graphical_analysis.logan_analysis_with_rsquared() petpal.kinetic_modeling.graphical_analysis.logan_ref_region_analysis() petpal.kinetic_modeling.graphical_analysis.logan_ref_region_analysis_with_rsquared() petpal.kinetic_modeling.graphical_analysis.patlak_analysis() petpal.kinetic_modeling.graphical_analysis.patlak_analysis_with_rsquared() petpal.kinetic_modeling.parametric_images.apply_linearized_analysis_to_all_voxels() petpal.kinetic_modeling.parametric_images.apply_mrtm2_to_all_voxels() petpal.kinetic_modeling.parametric_images.apply_rtm2_to_all_voxels() petpal.kinetic_modeling.parametric_images.generate_cmrglc_parametric_image_from_ki_image() petpal.kinetic_modeling.parametric_images.generate_parametric_images_with_graphical_method() petpal.kinetic_modeling.parametric_images.parametric_refregion_analysis() petpal.kinetic_modeling.reference_tissue_models._calc_frtm_params_from_kinetic_params() petpal.kinetic_modeling.reference_tissue_models._calc_simplified_frtm_tac() petpal.kinetic_modeling.reference_tissue_models.calc_bp_from_mrtm2_2003_fit() petpal.kinetic_modeling.reference_tissue_models.calc_bp_from_mrtm_2003_fit() petpal.kinetic_modeling.reference_tissue_models.calc_bp_from_mrtm_original_fit() petpal.kinetic_modeling.reference_tissue_models.calc_frtm_tac() petpal.kinetic_modeling.reference_tissue_models.calc_k2prime_from_mrtm_2003_fit() petpal.kinetic_modeling.reference_tissue_models.calc_k2prime_from_mrtm_original_fit() petpal.kinetic_modeling.reference_tissue_models.calc_srtm_tac() petpal.kinetic_modeling.reference_tissue_models.fit_frtm2_to_tac() petpal.kinetic_modeling.reference_tissue_models.fit_frtm2_to_tac_with_bounds() petpal.kinetic_modeling.reference_tissue_models.fit_frtm_to_tac() petpal.kinetic_modeling.reference_tissue_models.fit_frtm_to_tac_with_bounds() petpal.kinetic_modeling.reference_tissue_models.fit_mrtm2_2003_to_tac() petpal.kinetic_modeling.reference_tissue_models.fit_mrtm_2003_to_tac() petpal.kinetic_modeling.reference_tissue_models.fit_mrtm_original_to_tac() petpal.kinetic_modeling.reference_tissue_models.fit_srtm2_to_tac() petpal.kinetic_modeling.reference_tissue_models.fit_srtm2_to_tac_with_bounds() petpal.kinetic_modeling.reference_tissue_models.fit_srtm_to_tac() petpal.kinetic_modeling.reference_tissue_models.fit_srtm_to_tac_with_bounds() petpal.kinetic_modeling.tac_fitting._get_fitting_params_for_tcm_func() petpal.kinetic_modeling.tac_fitting._get_number_of_fit_params_for_tcm_func() petpal.kinetic_modeling.tcms_as_convolutions.calc_convolution_with_check() petpal.kinetic_modeling.tcms_as_convolutions.discrete_convolution_with_exponential() petpal.kinetic_modeling.tcms_as_convolutions.gen_tac_1tcm_cpet_from_tac() petpal.kinetic_modeling.tcms_as_convolutions.gen_tac_2tcm_cpet_from_tac() petpal.kinetic_modeling.tcms_as_convolutions.gen_tac_2tcm_with_k4zero_cpet_from_tac() petpal.kinetic_modeling.tcms_as_convolutions.generate_tac_2tcm_with_k4zero_c1_from_tac() petpal.kinetic_modeling.tcms_as_convolutions.generate_tac_2tcm_with_k4zero_c2_from_tac() petpal.kinetic_modeling.tcms_as_convolutions.generate_tac_serial_2tcm_c1_from_tac() petpal.kinetic_modeling.tcms_as_convolutions.generate_tac_serial_2tcm_c2_from_tac() petpal.kinetic_modeling.tcms_as_convolutions.model_serial_1tcm_frame_avgd() petpal.kinetic_modeling.tcms_as_convolutions.model_serial_2tcm_frame_avgd() petpal.kinetic_modeling.tcms_as_convolutions.response_function_1tcm_c1() petpal.kinetic_modeling.tcms_as_convolutions.response_function_2tcm_with_k4zero_c1() petpal.kinetic_modeling.tcms_as_convolutions.response_function_2tcm_with_k4zero_c2() petpal.kinetic_modeling.tcms_as_convolutions.response_function_serial_2tcm_c1() petpal.kinetic_modeling.tcms_as_convolutions.response_function_serial_2tcm_c2() petpal.meta.auto_cli.args_kwargs_to_dictionary() petpal.meta.auto_cli.auto_cli() petpal.meta.auto_cli.camel_to_kebab_case() petpal.meta.auto_cli.type_identifier() petpal.preproc.brain_mask_pet.brain_mask_pet() petpal.preproc.decay_correction.calculate_frame_decay_factor() petpal.preproc.decay_correction.decay_correct() petpal.preproc.decay_correction.scale_frames() petpal.preproc.decay_correction.undo_decay_correction() petpal.preproc.image_operations_4d.binarize_image_with_threshold() petpal.preproc.image_operations_4d.crop_image() petpal.preproc.image_operations_4d.extract_mean_roi_tac_from_nifti_using_segmentation() petpal.preproc.image_operations_4d.gauss_blur() petpal.preproc.image_operations_4d.rescale_image() petpal.preproc.image_operations_4d.roi_tac() petpal.preproc.image_operations_4d.stitch_broken_scans() petpal.preproc.image_operations_4d.threshold() petpal.preproc.motion_corr.windowed_motion_corr_to_target() petpal.preproc.motion_target.determine_motion_target() petpal.preproc.regional_tac_extraction.apply_mask_4d() petpal.preproc.regional_tac_extraction.extract_roi_voxel_tacs_from_image_using_mask() petpal.preproc.regional_tac_extraction.roi_tac() petpal.preproc.regional_tac_extraction.voxel_average_w_uncertainty() petpal.preproc.regional_tac_extraction.write_tacs() petpal.preproc.register.apply_xfm_ants() petpal.preproc.register.apply_xfm_fsl() petpal.preproc.register.register_pet() petpal.preproc.register.register_pet_to_pet() petpal.preproc.register.resample_nii_4dfp() petpal.preproc.register.warp_pet_to_atlas() petpal.preproc.segmentation_tools.binarize() petpal.preproc.segmentation_tools.calc_vesselness_mask_from_quantiled_vesselness() petpal.preproc.segmentation_tools.calc_vesselness_measure_image() petpal.preproc.segmentation_tools.combine_regions_as_mask() petpal.preproc.segmentation_tools.eroded_wm_segmentation() petpal.preproc.segmentation_tools.gw_segmentation() petpal.preproc.segmentation_tools.parcellate_right_left() petpal.preproc.segmentation_tools.replace_probabilistic_region() petpal.preproc.segmentation_tools.resample_segmentation() petpal.preproc.segmentation_tools.seg_crop_to_pet_fov() petpal.preproc.segmentation_tools.segmentations_merge() petpal.preproc.segmentation_tools.subcortical_mask() petpal.preproc.segmentation_tools.unique_segmentation_labels() petpal.preproc.segmentation_tools.vat_wm_ref_region() petpal.preproc.segmentation_tools.vat_wm_region_merge() petpal.preproc.standard_uptake_value.suv() petpal.preproc.standard_uptake_value.suvr() petpal.preproc.standard_uptake_value.weighted_sum_for_suv() petpal.utils.bids_utils.add_description_to_bids_path() petpal.utils.bids_utils.gen_bids_like_dir_path() petpal.utils.bids_utils.gen_bids_like_filename() petpal.utils.bids_utils.gen_bids_like_filepath() petpal.utils.bids_utils.parse_path_to_get_subject_and_session_id() petpal.utils.bids_utils.snake_to_camel_case() petpal.utils.bids_utils.validate_directory_as_bids() petpal.utils.bids_utils.validate_filepath_as_bids() petpal.utils.data_driven_image_analyses._gen_reshaped_quantiled_tacs() petpal.utils.data_driven_image_analyses._generate_quantiled_multi_tacs_header() petpal.utils.data_driven_image_analyses.extract_temporal_pca_components_of_image_over_mask() petpal.utils.data_driven_image_analyses.extract_temporal_pca_projection_of_image_over_mask() petpal.utils.data_driven_image_analyses.extract_temporal_pca_quantile_thresholded_tacs_of_image_using_mask() petpal.utils.data_driven_image_analyses.generate_temporal_pca_quantile_threshold_tacs_of_image_over_mask() petpal.utils.data_driven_image_analyses.temporal_pca_analysis_of_image_over_mask() petpal.utils.decorators.ANTsImageToANTsImage() petpal.utils.dimension.check_physical_space_for_ants_image_pair() petpal.utils.dimension.gen_3d_img_from_timeseries() petpal.utils.dimension.gen_nd_image_based_on_image_list() petpal.utils.dimension.get_frame_from_timeseries() petpal.utils.dimension.timeseries_from_img_list() petpal.utils.image_io.flatten_metadata() petpal.utils.image_io.gen_meta_data_filepath_for_nifti() petpal.utils.image_io.get_half_life_from_meta() petpal.utils.image_io.get_half_life_from_nifti() petpal.utils.image_io.get_half_life_from_radionuclide() petpal.utils.image_io.infer_sub_ses_from_tac_path() petpal.utils.image_io.km_regional_fits_to_tsv() petpal.utils.image_io.load_metadata_for_nifti_with_same_filename() petpal.utils.image_io.read_label_map_tsv() petpal.utils.image_io.safe_copy_meta() petpal.utils.image_io.safe_load_4dpet_nifti() petpal.utils.image_io.safe_load_meta() petpal.utils.image_io.validate_two_images_same_dimensions() petpal.utils.image_io.write_dict_to_json() petpal.utils.math_lib.gauss_blur_computation() petpal.utils.math_lib.weighted_sum_computation() petpal.utils.math_lib.weighted_sum_computation_over_index_window() petpal.utils.scan_timing.calculate_frame_reference_time() petpal.utils.scan_timing.get_window_index_pairs_for_image() petpal.utils.scan_timing.get_window_index_pairs_from_durations() petpal.utils.stats.mean_value_in_region() petpal.utils.testing_utils.add_gaussian_noise_to_tac_based_on_max() petpal.utils.testing_utils.bland_atlman_figure() petpal.utils.testing_utils.generate_random_parameter_samples() petpal.utils.testing_utils.ratio_bland_atlman_figure() petpal.utils.testing_utils.scatter_with_regression_figure() petpal.utils.time_activity_curve.get_frame_averaged_tac_vals() petpal.utils.time_activity_curve.get_frame_index_pairs_from_fine_times() petpal.utils.time_activity_curve.safe_load_tac() petpal.utils.time_activity_curve.safe_write_tac() petpal.utils.useful_functions.abbreviate_region() petpal.utils.useful_functions.build_label_map() petpal.utils.useful_functions.capitalize_first_char_of_str() petpal.utils.useful_functions.coerce_outpath_extension() petpal.utils.useful_functions.convert_ctab_to_dseg() petpal.utils.useful_functions.get_average_of_timeseries() petpal.utils.useful_functions.make_path() petpal.utils.useful_functions.nearest_frame_to_timepoint() petpal.utils.useful_functions.read_plasma_glucose_concentration() petpal.utils.useful_functions.str_to_camel_case() petpal.utils.useful_functions.weighted_series_sum() petpal.utils.useful_functions.weighted_series_sum_over_window_indices() petpal.visualizations.qc_plots.motion_plot() C calc_blood_input_function() (petpal.input_function.blood_input.BloodInputFunction method) calculate_analysis_properties() (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) calculate_dt_for_even_spacing_with_max_sampled() (petpal.kinetic_modeling.tac_interpolation.EvenlyInterpolateWithMax static method) calculate_filter_flags_and_signs() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase method) calculate_fit() (petpal.kinetic_modeling.graphical_analysis.GraphicalAnalysis method) (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis method) calculate_fit_params() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) calculate_fit_properties() (petpal.kinetic_modeling.graphical_analysis.GraphicalAnalysis method) (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis method) (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis method) calculate_intercept_image_properties() (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) calculate_parametric_images() (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) calculate_parametric_images_properties() (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) calculate_slope_image_properties() (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) calculate_tacs_from_mask() (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase method) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF method) calculate_top_pc_voxels_mask() (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF static method) calculate_valid_indicies_and_x_and_y() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) calculate_voxel_mask_from_quantiles() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter static method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase static method) calculated_uncertainty (petpal.kinetic_modeling.tac_uncertainty.TacUncertainty property) can_potentially_run() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) can_steps_potentially_run() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) capitalize_first_char_of_str() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis static method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis static method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin static method) (petpal.visualizations.tac_plots.RegionalTacFigure static method) center_in_mins (petpal.utils.scan_timing.ScanTimingInfo property) constant_uncertainty (petpal.kinetic_modeling.tac_uncertainty.TacUncertainty property) contains_any_nan (petpal.utils.time_activity_curve.TimeActivityCurve property) CONVERT_kBq_to_mCi_ (in module petpal.utils.constants) D decay_correct_factor_from_file() (petpal.preproc.decay_correction.DecayCorrect method) (petpal.preproc.decay_correction.DecayFix method) default_1tcm() (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep class method) default_alt_logan() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep class method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep class method) default_bids_pipeline() (petpal.pipelines.pipelines.BIDS_Pipeline class method) default_graphical_analysis_steps() (petpal.pipelines.steps_containers.StepsContainer class method) default_irreversible_2tcm() (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep class method) default_kinetic_analysis_steps() (petpal.pipelines.steps_containers.StepsContainer class method) default_logan() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep class method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep class method) default_logan_ref() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep class method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep class method) default_parametric_graphical_analysis_steps() (petpal.pipelines.steps_containers.StepsContainer class method) default_patlak() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep class method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep class method) default_pca_guided_idif_fit() (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep class method) default_pca_guided_idif_top_voxels() (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep class method) default_preprocess_steps() (petpal.pipelines.steps_containers.StepsContainer class method) default_reg_kwargs (petpal.preproc.motion_corr.MotionCorrect property) (petpal.preproc.register.RegisterBase property) (petpal.preproc.register.RegisterPet property) default_register_pet_to_t1() (petpal.pipelines.preproc_steps.ImageToImageStep class method) default_resample_blood_tac_on_scanner_times() (petpal.pipelines.preproc_steps.ResampleBloodTACStep class method) default_rescale_image() (petpal.pipelines.preproc_steps.ImageToImageStep class method) default_serial2tcm() (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep class method) default_steps_pipeline() (petpal.pipelines.pipelines.BIDS_Pipeline class method) (petpal.pipelines.steps_containers.StepsPipeline class method) default_tcm_analysis_steps() (petpal.pipelines.steps_containers.StepsContainer class method) default_threshold_cropping() (petpal.pipelines.preproc_steps.ImageToImageStep class method) default_warp_pet_to_atlas() (petpal.pipelines.preproc_steps.ImageToImageStep class method) default_windowed_moco() (petpal.pipelines.preproc_steps.ImageToImageStep class method) default_write_tacs_from_segmentation_rois() (petpal.pipelines.preproc_steps.TACsFromSegmentationStep class method) derivatives_dir (petpal.pipelines.pipelines.BIDS_Pipeline property) (petpal.pipelines.pipelines.BIDSyPathsForPipelines property) (petpal.pipelines.pipelines.BIDSyPathsForRawData property) detect_option() (petpal.meta.label_maps.LabelMapLoader method) duration_in_mins (petpal.utils.scan_timing.ScanTimingInfo property) E end_in_mins (petpal.utils.scan_timing.ScanTimingInfo property) evenly_resampled_tac() (petpal.utils.time_activity_curve.TimeActivityCurve method) evenly_resampled_tac_given_dt() (petpal.utils.time_activity_curve.TimeActivityCurve method) execute() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) (petpal.pipelines.steps_base.StepsAPI method) extract_header_from_nii() (petpal.utils.image_io.ImageIO method) extract_image_from_nii_as_numpy() (petpal.utils.image_io.ImageIO method) extract_np_to_ants() (petpal.utils.image_io.ImageIO method) extract_np_to_nibabel() (petpal.utils.image_io.ImageIO method) extract_tac() (petpal.preproc.regional_tac_extraction.WriteRegionalTacs method) F find_label_name() (petpal.preproc.regional_tac_extraction.WriteRegionalTacs method) fit_tac_to_model() (petpal.kinetic_modeling.fit_tac_with_rtms.FitTACWithRTMs method) fitting_func() (petpal.kinetic_modeling.tac_fitting.TACFitter method) (petpal.kinetic_modeling.tac_fitting.TACFitterWithoutBloodVolume method) fix_factor() (petpal.preproc.decay_correction.DecayFix method) format_usage() (petpal.meta.auto_cli.ParseKwargs method) frame_target() (petpal.preproc.motion_target.MotionTarget method) from_dict() (petpal.meta.label_maps.LabelMapLoader method) from_dseg_tsv() (petpal.meta.label_maps.LabelMapLoader method) from_json() (petpal.meta.label_maps.LabelMapLoader method) from_metadata() (petpal.utils.scan_timing.ScanTimingInfo class method) from_nifti() (petpal.utils.scan_timing.ScanTimingInfo class method) from_petpal() (petpal.meta.label_maps.LabelMapLoader method) from_start_end() (petpal.utils.scan_timing.ScanTimingInfo class method) from_tsv() (petpal.utils.time_activity_curve.TimeActivityCurve class method) FULL_NAME (in module petpal.utils.useful_functions) G gen_fit_params() (petpal.kinetic_modeling.tac_fitting.FrameAveragedTACFitter method) gen_legend() (petpal.visualizations.tac_plots.RegionalTacFigure method) (petpal.visualizations.tac_plots.TacFigure method) gen_line_profile() (petpal.preproc.image_operations_4d.SimpleAutoImageCropper static method) gen_tacs_data_frame() (petpal.preproc.regional_tac_extraction.WriteRegionalTacs method) generate_analysis_dirs() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.pipelines.BIDSyPathsForPipelines method) generate_figure() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) generate_figure_and_axes() (petpal.visualizations.graphical_plots.AltLoganPlot static method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot static method) (petpal.visualizations.graphical_plots.LoganPlot static method) (petpal.visualizations.graphical_plots.PatlakPlot static method) generate_kwargs_from_args() (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) generate_label_from_fit_params() (petpal.visualizations.graphical_plots.AltLoganPlot method) (petpal.visualizations.graphical_plots.GraphicalAnalysisPlot method) (petpal.visualizations.graphical_plots.LoganPlot method) (petpal.visualizations.graphical_plots.PatlakPlot method) get_args_not_set_in_kwargs() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep static method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep static method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep static method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep static method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep static method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep static method) (petpal.pipelines.steps_base.ObjectBasedStep static method) get_cropped_image() (petpal.preproc.image_operations_4d.SimpleAutoImageCropper static method) get_empty_default_kwargs() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) get_failed_output_nan_array() (petpal.kinetic_modeling.fit_tac_with_rtms.FitTACWithRTMs method) get_function_args_not_set_in_kwargs() (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) get_index_pairs_for_all_dims() (petpal.preproc.image_operations_4d.SimpleAutoImageCropper static method) get_left_and_right_boundary_indices_for_threshold() (petpal.preproc.image_operations_4d.SimpleAutoImageCropper static method) get_omega_matrix() (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm static method) get_pca_component_filter_flags() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter static method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase static method) get_pca_filter_signs_from_flags() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter static method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase static method) get_resampled_tac() (petpal.kinetic_modeling.tac_interpolation.EvenlyInterpolate method) (petpal.kinetic_modeling.tac_interpolation.EvenlyInterpolateWithMax method) get_stats() (petpal.utils.stats.RegionalStats method) get_step_from_node_label() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) get_steps_potential_run_state() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) get_tacs_list_from_dir() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis static method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis static method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin static method) (petpal.visualizations.tac_plots.RegionalTacFigure static method) get_tacs_objects_dict_from_dir() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis static method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis static method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin static method) (petpal.visualizations.tac_plots.RegionalTacFigure static method) get_tacs_objects_dict_from_files_list() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis static method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis static method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin static method) (petpal.visualizations.tac_plots.RegionalTacFigure static method) get_tacs_objects_list_from_files_list() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis static method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis static method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin static method) (petpal.visualizations.tac_plots.RegionalTacFigure static method) get_tacs_vals_from_dir() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin method) (petpal.visualizations.tac_plots.RegionalTacFigure method) get_tacs_vals_from_objs_list() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis static method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis static method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin static method) (petpal.visualizations.tac_plots.RegionalTacFigure static method) get_voxel_by_roi_matrix() (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm static method) get_voxels() (petpal.utils.stats.RegionalStats method) H HALF_LIVES (in module petpal.utils.constants) I idif_tac (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase property) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF property) idif_tac_werr (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase property) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF property) infer_output_directory_from_input_tac_path() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) infer_outputs_from_inputs() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) (petpal.pipelines.steps_base.StepsAPI method) infer_prefix_from_input_tac_path() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) infer_segmentation_label_from_tac_path() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis static method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis static method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin static method) (petpal.visualizations.tac_plots.RegionalTacFigure static method) infer_segmentation_labels_for_tacs() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin method) (petpal.visualizations.tac_plots.RegionalTacFigure method) init_analysis_props() (petpal.kinetic_modeling.graphical_analysis.GraphicalAnalysis method) (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis method) (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) (petpal.kinetic_modeling.parametric_images.ReferenceTissueParametricImage method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis method) input_image_path (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep property) (petpal.pipelines.preproc_steps.ResampleBloodTACStep property) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep property) input_tac_path (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis property) (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin property) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep property) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin property) (petpal.visualizations.tac_plots.RegionalTacFigure property) is_empty_region() (petpal.preproc.regional_tac_extraction.WriteRegionalTacs method) is_valid_tacs_dir() (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin method) (petpal.visualizations.tac_plots.RegionalTacFigure method) K KMStepType (in module petpal.pipelines.kinetic_modeling_steps) L label_map_freesurfer (in module petpal.meta.label_maps) label_map_freesurfer_merge_lr (in module petpal.meta.label_maps) label_map_perlcyno (in module petpal.meta.label_maps) label_map_perlcyno_merge_lr (in module petpal.meta.label_maps) labels_to_camel_case() (petpal.meta.label_maps.LabelMapLoader method) left_shifted_tac() (petpal.utils.time_activity_curve.TimeActivityCurve static method) linear_fitting_func() (petpal.input_function.blood_input.BloodInputFunction static method) load() (petpal.io.image.ImageLoader method) log_cli_args() (petpal.meta.auto_cli.PetpalLogging method) M make_analysis_dirs() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.pipelines.BIDSyPathsForPipelines method) make_first_frame() (petpal.visualizations.image_visualization.NiftiGifCreator method) make_gif() (petpal.visualizations.image_visualization.NiftiGifCreator method) mask_image_path (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep property) max (petpal.utils.stats.RegionalStats property) mean (petpal.utils.stats.RegionalStats property) mean_target() (petpal.preproc.motion_target.MotionTarget method) median (petpal.utils.stats.RegionalStats property) method (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep property) min (petpal.utils.stats.RegionalStats property) module petpal petpal.cli petpal.cli.cli_graphical_analysis petpal.cli.cli_graphical_plots petpal.cli.cli_idif petpal.cli.cli_parametric_images petpal.cli.cli_pib_processing petpal.cli.cli_plot_tacs petpal.cli.cli_preproc petpal.cli.cli_pvc petpal.cli.cli_reference_tissue_models petpal.cli.cli_stats petpal.cli.cli_tac_fitting petpal.cli.cli_tac_interpolation petpal.cli.cli_vat_processing petpal.input_function petpal.input_function.blood_input petpal.input_function.idif_necktangle petpal.input_function.pca_guided_idif petpal.io petpal.io.image petpal.io.table petpal.kinetic_modeling petpal.kinetic_modeling.fit_tac_with_rtms petpal.kinetic_modeling.graphical_analysis petpal.kinetic_modeling.parametric_images petpal.kinetic_modeling.reference_tissue_models petpal.kinetic_modeling.rtm_analysis petpal.kinetic_modeling.tac_fitting petpal.kinetic_modeling.tac_interpolation petpal.kinetic_modeling.tac_uncertainty petpal.kinetic_modeling.tcms_as_convolutions petpal.meta petpal.meta.auto_cli petpal.meta.label_maps petpal.pipelines petpal.pipelines.kinetic_modeling_steps petpal.pipelines.pca_guided_idif_steps petpal.pipelines.pipelines petpal.pipelines.preproc_steps petpal.pipelines.steps_base petpal.pipelines.steps_containers petpal.preproc petpal.preproc.brain_mask_pet petpal.preproc.decay_correction petpal.preproc.image_operations_4d petpal.preproc.motion_corr petpal.preproc.motion_target petpal.preproc.partial_volume_corrections petpal.preproc.regional_tac_extraction petpal.preproc.register petpal.preproc.segmentation_tools petpal.preproc.standard_uptake_value petpal.preproc.symmetric_geometric_transfer_matrix petpal.utils petpal.utils.bids_utils petpal.utils.constants petpal.utils.data_driven_image_analyses petpal.utils.decorators petpal.utils.dimension petpal.utils.image_io petpal.utils.math_lib petpal.utils.metadata petpal.utils.scan_timing petpal.utils.stats petpal.utils.testing_utils petpal.utils.time_activity_curve petpal.utils.useful_functions petpal.visualizations petpal.visualizations.graphical_plots petpal.visualizations.image_visualization petpal.visualizations.qc_plots petpal.visualizations.tac_plots N nifty_loader (in module petpal.visualizations.image_visualization) normalize_name() (petpal.kinetic_modeling.tac_fitting.ConvTcmModelConfig static method) (petpal.kinetic_modeling.tac_fitting.FrameAvgdTcmModelConfig static method) (petpal.kinetic_modeling.tac_fitting.TcmModelConfig static method) num_of_voxels (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep property) num_pca_components (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep property) nvox (petpal.utils.stats.RegionalStats property) O out_path_and_prefix (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin property) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep property) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep property) out_tacs_dir (petpal.pipelines.preproc_steps.TACsFromSegmentationStep property) out_tacs_prefix (petpal.pipelines.preproc_steps.TACsFromSegmentationStep property) output_directory (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin property) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep property) output_prefix (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin property) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep property) output_tac_path (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep property) P pca_comp_filter_flag_threshold (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase property) pca_comp_filter_min_val (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase property) perform_temporal_pca() (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase method) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF method) pet_path (petpal.pipelines.pipelines.BIDS_Pipeline property) (petpal.pipelines.pipelines.BIDSyPathsForPipelines property) (petpal.pipelines.pipelines.BIDSyPathsForRawData property) petpal module petpal.cli module petpal.cli.cli_graphical_analysis module petpal.cli.cli_graphical_analysis._add_common_args() built-in function petpal.cli.cli_graphical_plots module petpal.cli.cli_idif module petpal.cli.cli_parametric_images module petpal.cli.cli_pib_processing module petpal.cli.cli_plot_tacs module petpal.cli.cli_preproc module petpal.cli.cli_preproc._add_common_args() built-in function petpal.cli.cli_preproc._generate_args() built-in function petpal.cli.cli_pvc module petpal.cli.cli_pvc.sgtm_cli_run() built-in function petpal.cli.cli_reference_tissue_models module petpal.cli.cli_reference_tissue_models._generate_bounds() built-in function petpal.cli.cli_reference_tissue_models._pretty_print_results() built-in function petpal.cli.cli_reference_tissue_models.add_common_args() built-in function petpal.cli.cli_reference_tissue_models.parse_args() built-in function petpal.cli.cli_stats module petpal.cli.cli_tac_fitting module petpal.cli.cli_tac_fitting._generate_args() built-in function petpal.cli.cli_tac_fitting._generate_bounds() built-in function petpal.cli.cli_tac_fitting.add_common_analysis_args() built-in function petpal.cli.cli_tac_fitting.add_common_io_args() built-in function petpal.cli.cli_tac_fitting.add_common_print_args() built-in function petpal.cli.cli_tac_fitting.fit_props_printer() built-in function petpal.cli.cli_tac_interpolation module petpal.cli.cli_tac_interpolation._print_tac_to_screen() built-in function petpal.cli.cli_tac_interpolation._safe_write_tac() built-in function petpal.cli.cli_vat_processing module petpal.cli.cli_vat_processing.infer_group() built-in function petpal.cli.cli_vat_processing.rename_subs() built-in function petpal.cli.cli_vat_processing.vat_protocol() built-in function petpal.input_function module petpal.input_function.blood_input module petpal.input_function.blood_input.BloodInputFunction (built-in class) petpal.input_function.blood_input.extract_blood_input_function_activity_from_csv() built-in function petpal.input_function.blood_input.extract_blood_input_function_from_csv() built-in function petpal.input_function.blood_input.extract_blood_input_function_times_from_csv() built-in function petpal.input_function.blood_input.read_plasma_glucose_concentration() built-in function petpal.input_function.blood_input.resample_blood_data_on_scanner_times() built-in function petpal.input_function.idif_necktangle module petpal.input_function.idif_necktangle.average_across_4d_frames() built-in function petpal.input_function.idif_necktangle.double_threshold_idif_from_4d_pet_necktangle() built-in function petpal.input_function.idif_necktangle.get_frame_time_midpoints() built-in function petpal.input_function.idif_necktangle.load_fslmeants_to_numpy_3d() built-in function petpal.input_function.idif_necktangle.single_threshold_idif_from_4d_pet_with_necktangle() built-in function petpal.input_function.pca_guided_idif module petpal.input_function.pca_guided_idif.PCAGuidedIdifBase (built-in class) petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter (built-in class) petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase (built-in class) petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF (built-in class) petpal.io module petpal.io.image module petpal.io.image.ImageLoader (built-in class) petpal.io.table module petpal.io.table.get_tabular_separator() built-in function petpal.io.table.TableSaver (built-in class) petpal.kinetic_modeling module petpal.kinetic_modeling.fit_tac_with_rtms module petpal.kinetic_modeling.fit_tac_with_rtms.FitTACWithRTMs (built-in class) petpal.kinetic_modeling.fit_tac_with_rtms.get_rtm_kwargs() built-in function petpal.kinetic_modeling.fit_tac_with_rtms.get_rtm_method() built-in function petpal.kinetic_modeling.fit_tac_with_rtms.get_rtm_output_size() built-in function petpal.kinetic_modeling.graphical_analysis module petpal.kinetic_modeling.graphical_analysis._line_fitting_make_rhs_matrix_from_xdata() built-in function petpal.kinetic_modeling.graphical_analysis.alternative_logan_analysis() built-in function petpal.kinetic_modeling.graphical_analysis.alternative_logan_analysis_with_rsquared() built-in function petpal.kinetic_modeling.graphical_analysis.calculate_patlak_x() built-in function petpal.kinetic_modeling.graphical_analysis.cumulative_trapezoidal_integral() built-in function petpal.kinetic_modeling.graphical_analysis.fit_line_to_data_using_lls() built-in function petpal.kinetic_modeling.graphical_analysis.fit_line_to_data_using_lls_with_rsquared() built-in function petpal.kinetic_modeling.graphical_analysis.get_graphical_analysis_method() built-in function petpal.kinetic_modeling.graphical_analysis.get_graphical_analysis_method_with_rsquared() built-in function petpal.kinetic_modeling.graphical_analysis.get_index_from_threshold() built-in function petpal.kinetic_modeling.graphical_analysis.GraphicalAnalysis (built-in class) petpal.kinetic_modeling.graphical_analysis.km_multifit_analysis_to_jsons() built-in function petpal.kinetic_modeling.graphical_analysis.km_multifit_analysis_to_tsv() built-in function petpal.kinetic_modeling.graphical_analysis.linear_least_squares_fit_with_stats() built-in function petpal.kinetic_modeling.graphical_analysis.logan_analysis() built-in function petpal.kinetic_modeling.graphical_analysis.logan_analysis_with_rsquared() built-in function petpal.kinetic_modeling.graphical_analysis.logan_ref_region_analysis() built-in function petpal.kinetic_modeling.graphical_analysis.logan_ref_region_analysis_with_rsquared() built-in function petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis (built-in class) petpal.kinetic_modeling.graphical_analysis.patlak_analysis() built-in function petpal.kinetic_modeling.graphical_analysis.patlak_analysis_with_rsquared() built-in function petpal.kinetic_modeling.parametric_images module petpal.kinetic_modeling.parametric_images.apply_linearized_analysis_to_all_voxels() built-in function petpal.kinetic_modeling.parametric_images.apply_mrtm2_to_all_voxels() built-in function petpal.kinetic_modeling.parametric_images.apply_rtm2_to_all_voxels() built-in function petpal.kinetic_modeling.parametric_images.generate_cmrglc_parametric_image_from_ki_image() built-in function petpal.kinetic_modeling.parametric_images.generate_parametric_images_with_graphical_method() built-in function petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage (built-in class) petpal.kinetic_modeling.parametric_images.parametric_refregion_analysis() built-in function petpal.kinetic_modeling.parametric_images.ReferenceTissueParametricImage (built-in class) petpal.kinetic_modeling.reference_tissue_models module petpal.kinetic_modeling.reference_tissue_models._calc_frtm_params_from_kinetic_params() built-in function petpal.kinetic_modeling.reference_tissue_models._calc_simplified_frtm_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.calc_bp_from_mrtm2_2003_fit() built-in function petpal.kinetic_modeling.reference_tissue_models.calc_bp_from_mrtm_2003_fit() built-in function petpal.kinetic_modeling.reference_tissue_models.calc_bp_from_mrtm_original_fit() built-in function petpal.kinetic_modeling.reference_tissue_models.calc_frtm_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.calc_k2prime_from_mrtm_2003_fit() built-in function petpal.kinetic_modeling.reference_tissue_models.calc_k2prime_from_mrtm_original_fit() built-in function petpal.kinetic_modeling.reference_tissue_models.calc_srtm_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_frtm2_to_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_frtm2_to_tac_with_bounds() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_frtm_to_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_frtm_to_tac_with_bounds() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_mrtm2_2003_to_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_mrtm_2003_to_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_mrtm_original_to_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_srtm2_to_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_srtm2_to_tac_with_bounds() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_srtm_to_tac() built-in function petpal.kinetic_modeling.reference_tissue_models.fit_srtm_to_tac_with_bounds() built-in function petpal.kinetic_modeling.rtm_analysis module petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis (built-in class) petpal.kinetic_modeling.rtm_analysis.RTMAnalysis (built-in class) petpal.kinetic_modeling.tac_fitting module petpal.kinetic_modeling.tac_fitting._get_fitting_params_for_tcm_func() built-in function petpal.kinetic_modeling.tac_fitting._get_number_of_fit_params_for_tcm_func() built-in function petpal.kinetic_modeling.tac_fitting.ConvTcmModelConfig (built-in class) petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis (built-in class) petpal.kinetic_modeling.tac_fitting.FrameAveragedTACFitter (built-in class) petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis (built-in class) petpal.kinetic_modeling.tac_fitting.FrameAvgdTcmModelConfig (built-in class) petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis (built-in class) petpal.kinetic_modeling.tac_fitting.TACFitter (built-in class) petpal.kinetic_modeling.tac_fitting.TACFitterWithoutBloodVolume (built-in class) petpal.kinetic_modeling.tac_fitting.TCMAnalysis (built-in class) petpal.kinetic_modeling.tac_fitting.TcmModelConfig (built-in class) petpal.kinetic_modeling.tac_interpolation module petpal.kinetic_modeling.tac_interpolation.EvenlyInterpolate (built-in class) petpal.kinetic_modeling.tac_interpolation.EvenlyInterpolateWithMax (built-in class) petpal.kinetic_modeling.tac_uncertainty module petpal.kinetic_modeling.tac_uncertainty.TacUncertainty (built-in class) petpal.kinetic_modeling.tcms_as_convolutions module petpal.kinetic_modeling.tcms_as_convolutions.calc_convolution_with_check() built-in function petpal.kinetic_modeling.tcms_as_convolutions.discrete_convolution_with_exponential() built-in function petpal.kinetic_modeling.tcms_as_convolutions.gen_tac_1tcm_cpet_from_tac() built-in function petpal.kinetic_modeling.tcms_as_convolutions.gen_tac_2tcm_cpet_from_tac() built-in function petpal.kinetic_modeling.tcms_as_convolutions.gen_tac_2tcm_with_k4zero_cpet_from_tac() built-in function petpal.kinetic_modeling.tcms_as_convolutions.generate_tac_2tcm_with_k4zero_c1_from_tac() built-in function petpal.kinetic_modeling.tcms_as_convolutions.generate_tac_2tcm_with_k4zero_c2_from_tac() built-in function petpal.kinetic_modeling.tcms_as_convolutions.generate_tac_serial_2tcm_c1_from_tac() built-in function petpal.kinetic_modeling.tcms_as_convolutions.generate_tac_serial_2tcm_c2_from_tac() built-in function petpal.kinetic_modeling.tcms_as_convolutions.model_serial_1tcm_frame_avgd() built-in function petpal.kinetic_modeling.tcms_as_convolutions.model_serial_2tcm_frame_avgd() built-in function petpal.kinetic_modeling.tcms_as_convolutions.response_function_1tcm_c1() built-in function petpal.kinetic_modeling.tcms_as_convolutions.response_function_2tcm_with_k4zero_c1() built-in function petpal.kinetic_modeling.tcms_as_convolutions.response_function_2tcm_with_k4zero_c2() built-in function petpal.kinetic_modeling.tcms_as_convolutions.response_function_serial_2tcm_c1() built-in function petpal.kinetic_modeling.tcms_as_convolutions.response_function_serial_2tcm_c2() built-in function petpal.meta module petpal.meta.auto_cli module petpal.meta.auto_cli.args_kwargs_to_dictionary() built-in function petpal.meta.auto_cli.auto_cli() built-in function petpal.meta.auto_cli.camel_to_kebab_case() built-in function petpal.meta.auto_cli.ParseKwargs (built-in class) petpal.meta.auto_cli.PetpalLogging (built-in class) petpal.meta.auto_cli.type_identifier() built-in function petpal.meta.label_maps module petpal.meta.label_maps.LabelMapLoader (built-in class) petpal.pipelines module petpal.pipelines.kinetic_modeling_steps module petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep (built-in class) petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep (built-in class) petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep (built-in class) petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin (built-in class) petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep (built-in class) petpal.pipelines.pca_guided_idif_steps module petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep (built-in class) petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin (built-in class) petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep (built-in class) petpal.pipelines.pipelines module petpal.pipelines.pipelines.BIDS_Pipeline (built-in class) petpal.pipelines.pipelines.BIDSyPathsForPipelines (built-in class) petpal.pipelines.pipelines.BIDSyPathsForRawData (built-in class) petpal.pipelines.preproc_steps module petpal.pipelines.preproc_steps.ImagePairToArrayStep (built-in class) petpal.pipelines.preproc_steps.ImageToImageStep (built-in class) petpal.pipelines.preproc_steps.ResampleBloodTACStep (built-in class) petpal.pipelines.preproc_steps.TACsFromSegmentationStep (built-in class) petpal.pipelines.steps_base module petpal.pipelines.steps_base.ArgsDict (built-in class) petpal.pipelines.steps_base.FunctionBasedStep (built-in class) petpal.pipelines.steps_base.ObjectBasedStep (built-in class) petpal.pipelines.steps_base.StepsAPI (built-in class) petpal.pipelines.steps_containers module petpal.pipelines.steps_containers.StepsContainer (built-in class) petpal.pipelines.steps_containers.StepsPipeline (built-in class) petpal.preproc module petpal.preproc.brain_mask_pet module petpal.preproc.brain_mask_pet.brain_mask_pet() built-in function petpal.preproc.decay_correction module petpal.preproc.decay_correction.calculate_frame_decay_factor() built-in function petpal.preproc.decay_correction.decay_correct() built-in function petpal.preproc.decay_correction.DecayCorrect (built-in class) petpal.preproc.decay_correction.DecayFix (built-in class) petpal.preproc.decay_correction.scale_frames() built-in function petpal.preproc.decay_correction.undo_decay_correction() built-in function petpal.preproc.image_operations_4d module petpal.preproc.image_operations_4d.binarize_image_with_threshold() built-in function petpal.preproc.image_operations_4d.crop_image() built-in function petpal.preproc.image_operations_4d.extract_mean_roi_tac_from_nifti_using_segmentation() built-in function petpal.preproc.image_operations_4d.gauss_blur() built-in function petpal.preproc.image_operations_4d.rescale_image() built-in function petpal.preproc.image_operations_4d.roi_tac() built-in function petpal.preproc.image_operations_4d.SimpleAutoImageCropper (built-in class) petpal.preproc.image_operations_4d.stitch_broken_scans() built-in function petpal.preproc.image_operations_4d.threshold() built-in function petpal.preproc.motion_corr module petpal.preproc.motion_corr.MotionCorrect (built-in class) petpal.preproc.motion_corr.windowed_motion_corr_to_target() built-in function petpal.preproc.motion_target module petpal.preproc.motion_target.determine_motion_target() built-in function petpal.preproc.motion_target.MotionTarget (built-in class) petpal.preproc.partial_volume_corrections module petpal.preproc.partial_volume_corrections.PetPvc (built-in class) petpal.preproc.regional_tac_extraction module petpal.preproc.regional_tac_extraction.apply_mask_4d() built-in function petpal.preproc.regional_tac_extraction.extract_roi_voxel_tacs_from_image_using_mask() built-in function petpal.preproc.regional_tac_extraction.roi_tac() built-in function petpal.preproc.regional_tac_extraction.voxel_average_w_uncertainty() built-in function petpal.preproc.regional_tac_extraction.write_tacs() built-in function petpal.preproc.regional_tac_extraction.WriteRegionalTacs (built-in class) petpal.preproc.register module petpal.preproc.register.apply_xfm_ants() built-in function petpal.preproc.register.apply_xfm_fsl() built-in function petpal.preproc.register.register_pet() built-in function petpal.preproc.register.register_pet_to_pet() built-in function petpal.preproc.register.RegisterBase (built-in class) petpal.preproc.register.RegisterPet (built-in class) petpal.preproc.register.resample_nii_4dfp() built-in function petpal.preproc.register.warp_pet_to_atlas() built-in function petpal.preproc.segmentation_tools module petpal.preproc.segmentation_tools.binarize() built-in function petpal.preproc.segmentation_tools.calc_vesselness_mask_from_quantiled_vesselness() built-in function petpal.preproc.segmentation_tools.calc_vesselness_measure_image() built-in function petpal.preproc.segmentation_tools.combine_regions_as_mask() built-in function petpal.preproc.segmentation_tools.eroded_wm_segmentation() built-in function petpal.preproc.segmentation_tools.gw_segmentation() built-in function petpal.preproc.segmentation_tools.parcellate_right_left() built-in function petpal.preproc.segmentation_tools.replace_probabilistic_region() built-in function petpal.preproc.segmentation_tools.resample_segmentation() built-in function petpal.preproc.segmentation_tools.seg_crop_to_pet_fov() built-in function petpal.preproc.segmentation_tools.segmentations_merge() built-in function petpal.preproc.segmentation_tools.subcortical_mask() built-in function petpal.preproc.segmentation_tools.unique_segmentation_labels() built-in function petpal.preproc.segmentation_tools.vat_wm_ref_region() built-in function petpal.preproc.segmentation_tools.vat_wm_region_merge() built-in function petpal.preproc.standard_uptake_value module petpal.preproc.standard_uptake_value.suv() built-in function petpal.preproc.standard_uptake_value.suvr() built-in function petpal.preproc.standard_uptake_value.weighted_sum_for_suv() built-in function petpal.preproc.symmetric_geometric_transfer_matrix module petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm (built-in class) petpal.utils module petpal.utils.bids_utils module petpal.utils.bids_utils.add_description_to_bids_path() built-in function petpal.utils.bids_utils.gen_bids_like_dir_path() built-in function petpal.utils.bids_utils.gen_bids_like_filename() built-in function petpal.utils.bids_utils.gen_bids_like_filepath() built-in function petpal.utils.bids_utils.parse_path_to_get_subject_and_session_id() built-in function petpal.utils.bids_utils.snake_to_camel_case() built-in function petpal.utils.bids_utils.validate_directory_as_bids() built-in function petpal.utils.bids_utils.validate_filepath_as_bids() built-in function petpal.utils.constants module petpal.utils.data_driven_image_analyses module petpal.utils.data_driven_image_analyses._gen_reshaped_quantiled_tacs() built-in function petpal.utils.data_driven_image_analyses._generate_quantiled_multi_tacs_header() built-in function petpal.utils.data_driven_image_analyses.extract_temporal_pca_components_of_image_over_mask() built-in function petpal.utils.data_driven_image_analyses.extract_temporal_pca_projection_of_image_over_mask() built-in function petpal.utils.data_driven_image_analyses.extract_temporal_pca_quantile_thresholded_tacs_of_image_using_mask() built-in function petpal.utils.data_driven_image_analyses.generate_temporal_pca_quantile_threshold_tacs_of_image_over_mask() built-in function petpal.utils.data_driven_image_analyses.temporal_pca_analysis_of_image_over_mask() built-in function petpal.utils.decorators module petpal.utils.decorators.ANTsImageToANTsImage() built-in function petpal.utils.dimension module petpal.utils.dimension.check_physical_space_for_ants_image_pair() built-in function petpal.utils.dimension.gen_3d_img_from_timeseries() built-in function petpal.utils.dimension.gen_nd_image_based_on_image_list() built-in function petpal.utils.dimension.get_frame_from_timeseries() built-in function petpal.utils.dimension.timeseries_from_img_list() built-in function petpal.utils.image_io module petpal.utils.image_io.flatten_metadata() built-in function petpal.utils.image_io.gen_meta_data_filepath_for_nifti() built-in function petpal.utils.image_io.get_half_life_from_meta() built-in function petpal.utils.image_io.get_half_life_from_nifti() built-in function petpal.utils.image_io.get_half_life_from_radionuclide() built-in function petpal.utils.image_io.ImageIO (built-in class) petpal.utils.image_io.infer_sub_ses_from_tac_path() built-in function petpal.utils.image_io.km_regional_fits_to_tsv() built-in function petpal.utils.image_io.load_metadata_for_nifti_with_same_filename() built-in function petpal.utils.image_io.read_label_map_tsv() built-in function petpal.utils.image_io.safe_copy_meta() built-in function petpal.utils.image_io.safe_load_4dpet_nifti() built-in function petpal.utils.image_io.safe_load_meta() built-in function petpal.utils.image_io.validate_two_images_same_dimensions() built-in function petpal.utils.image_io.write_dict_to_json() built-in function petpal.utils.math_lib module petpal.utils.math_lib.gauss_blur_computation() built-in function petpal.utils.math_lib.weighted_sum_computation() built-in function petpal.utils.math_lib.weighted_sum_computation_over_index_window() built-in function petpal.utils.metadata module petpal.utils.metadata.BidsMetadataMender (built-in class) petpal.utils.scan_timing module petpal.utils.scan_timing.calculate_frame_reference_time() built-in function petpal.utils.scan_timing.get_window_index_pairs_for_image() built-in function petpal.utils.scan_timing.get_window_index_pairs_from_durations() built-in function petpal.utils.scan_timing.ScanTimingInfo (built-in class) petpal.utils.stats module petpal.utils.stats.mean_value_in_region() built-in function petpal.utils.stats.RegionalStats (built-in class) petpal.utils.testing_utils module petpal.utils.testing_utils.add_gaussian_noise_to_tac_based_on_max() built-in function petpal.utils.testing_utils.bland_atlman_figure() built-in function petpal.utils.testing_utils.generate_random_parameter_samples() built-in function petpal.utils.testing_utils.ratio_bland_atlman_figure() built-in function petpal.utils.testing_utils.scatter_with_regression_figure() built-in function petpal.utils.time_activity_curve module petpal.utils.time_activity_curve.get_frame_averaged_tac_vals() built-in function petpal.utils.time_activity_curve.get_frame_index_pairs_from_fine_times() built-in function petpal.utils.time_activity_curve.MultiTACAnalysisMixin (built-in class) petpal.utils.time_activity_curve.safe_load_tac() built-in function petpal.utils.time_activity_curve.safe_write_tac() built-in function petpal.utils.time_activity_curve.TimeActivityCurve (built-in class) petpal.utils.useful_functions module petpal.utils.useful_functions.abbreviate_region() built-in function petpal.utils.useful_functions.build_label_map() built-in function petpal.utils.useful_functions.capitalize_first_char_of_str() built-in function petpal.utils.useful_functions.coerce_outpath_extension() built-in function petpal.utils.useful_functions.convert_ctab_to_dseg() built-in function petpal.utils.useful_functions.get_average_of_timeseries() built-in function petpal.utils.useful_functions.make_path() built-in function petpal.utils.useful_functions.nearest_frame_to_timepoint() built-in function petpal.utils.useful_functions.read_plasma_glucose_concentration() built-in function petpal.utils.useful_functions.str_to_camel_case() built-in function petpal.utils.useful_functions.weighted_series_sum() built-in function petpal.utils.useful_functions.weighted_series_sum_over_window_indices() built-in function petpal.visualizations module petpal.visualizations.graphical_plots module petpal.visualizations.graphical_plots.AltLoganPlot (built-in class) petpal.visualizations.graphical_plots.GraphicalAnalysisPlot (built-in class) petpal.visualizations.graphical_plots.LoganPlot (built-in class) petpal.visualizations.graphical_plots.PatlakPlot (built-in class) petpal.visualizations.graphical_plots.Plot (built-in class) petpal.visualizations.image_visualization module petpal.visualizations.image_visualization.NiftiGifCreator (built-in class) petpal.visualizations.qc_plots module petpal.visualizations.qc_plots.motion_plot() built-in function petpal.visualizations.tac_plots module petpal.visualizations.tac_plots.RegionalTacFigure (built-in class) petpal.visualizations.tac_plots.TacFigure (built-in class) pipeline_dir (petpal.pipelines.pipelines.BIDS_Pipeline property) (petpal.pipelines.pipelines.BIDSyPathsForPipelines property) plot_all_regional_tacs() (petpal.visualizations.tac_plots.RegionalTacFigure method) plot_all_regional_tacs_with_errorbar() (petpal.visualizations.tac_plots.RegionalTacFigure method) plot_dependency_graph() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) plot_motion() (petpal.preproc.motion_corr.MotionCorrect method) plot_tacs_in_regions_list() (petpal.visualizations.tac_plots.RegionalTacFigure method) plot_tacs_in_regions_list_with_errorbar() (petpal.visualizations.tac_plots.RegionalTacFigure method) PreprocStepType (in module petpal.pipelines.preproc_steps) print_dependency_graph() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) print_step_details() (petpal.pipelines.steps_containers.StepsContainer method) print_steps_details() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) print_steps_names() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) prj_idif_tac (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase property) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF property) prj_idif_tac_werr (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter property) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase property) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF property) R raw_blood_tac_path (petpal.pipelines.preproc_steps.ResampleBloodTACStep property) reference_tac_path (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis property) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis property) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis property) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis property) (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin property) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep property) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin property) (petpal.visualizations.tac_plots.RegionalTacFigure property) register_target() (petpal.preproc.register.RegisterPet method) register_windows() (petpal.preproc.motion_corr.MotionCorrect method) remove_step() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsContainer method) (petpal.pipelines.steps_containers.StepsPipeline method) resample_tac_on_new_times() (petpal.kinetic_modeling.tac_fitting.TACFitter static method) (petpal.kinetic_modeling.tac_fitting.TACFitterWithoutBloodVolume static method) resample_tacs_evenly() (petpal.kinetic_modeling.tac_fitting.TACFitter method) (petpal.kinetic_modeling.tac_fitting.TACFitterWithoutBloodVolume method) resampled_tac_on_times() (petpal.utils.time_activity_curve.TimeActivityCurve method) resampled_tac_path (petpal.pipelines.preproc_steps.ResampleBloodTACStep property) rescale_tacs() (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase method) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF method) residual() (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase method) resolve_model_name() (petpal.kinetic_modeling.tac_fitting.ConvTcmModelConfig class method) (petpal.kinetic_modeling.tac_fitting.FrameAvgdTcmModelConfig class method) (petpal.kinetic_modeling.tac_fitting.TcmModelConfig class method) right_shifted_tac() (petpal.utils.time_activity_curve.TimeActivityCurve static method) roi_tacs_dir (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin property) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep property) run() (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase method) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF method) (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm method) run_analysis() (petpal.kinetic_modeling.graphical_analysis.GraphicalAnalysis method) (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis method) (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis method) run_fit() (petpal.kinetic_modeling.tac_fitting.FrameAveragedTACFitter method) (petpal.kinetic_modeling.tac_fitting.TACFitter method) (petpal.kinetic_modeling.tac_fitting.TACFitterWithoutBloodVolume method) run_parametric_analysis() (petpal.kinetic_modeling.parametric_images.ReferenceTissueParametricImage method) run_petpvc() (petpal.preproc.partial_volume_corrections.PetPvc method) run_sgtm_3d() (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm method) run_sgtm_4d() (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm method) S sanitize_tac() (petpal.kinetic_modeling.tac_fitting.TACFitter static method) (petpal.kinetic_modeling.tac_fitting.TACFitterWithoutBloodVolume static method) save() (petpal.input_function.pca_guided_idif.PCAGuidedIdifBase method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitter method) (petpal.input_function.pca_guided_idif.PCAGuidedIdifFitterBase method) (petpal.input_function.pca_guided_idif.PCAGuidedTopVoxelsIDIF method) (petpal.io.table.TableSaver method) (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm method) save_analysis() (petpal.kinetic_modeling.graphical_analysis.GraphicalAnalysis method) (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis method) (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis method) save_analysis_properties() (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) (petpal.kinetic_modeling.parametric_images.ReferenceTissueParametricImage method) save_figure() (petpal.visualizations.graphical_plots.Plot method) save_modified_pet() (petpal.preproc.decay_correction.DecayCorrect method) (petpal.preproc.decay_correction.DecayFix method) save_nii() (petpal.utils.image_io.ImageIO method) save_parametric_images() (petpal.kinetic_modeling.parametric_images.GraphicalAnalysisParametricImage method) (petpal.kinetic_modeling.parametric_images.ReferenceTissueParametricImage method) save_results_3d() (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm method) save_results_4d_multitacs() (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm method) save_results_4d_tacs() (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm method) save_xfm_parameters() (petpal.preproc.motion_corr.MotionCorrect method) seg_img (petpal.pipelines.pipelines.BIDS_Pipeline property) (petpal.pipelines.pipelines.BIDSyPathsForPipelines property) (petpal.pipelines.pipelines.BIDSyPathsForRawData property) seg_table (petpal.pipelines.pipelines.BIDS_Pipeline property) (petpal.pipelines.pipelines.BIDSyPathsForPipelines property) (petpal.pipelines.pipelines.BIDSyPathsForRawData property) segmentation_image_path (petpal.pipelines.preproc_steps.TACsFromSegmentationStep property) segmentation_label_map_path (petpal.pipelines.preproc_steps.TACsFromSegmentationStep property) selected_component (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep property) set_activity_non_negative() (petpal.utils.time_activity_curve.TimeActivityCurve method) set_analysis_props() (petpal.kinetic_modeling.parametric_images.ReferenceTissueParametricImage method) set_figure_title_and_labels() (petpal.visualizations.image_visualization.NiftiGifCreator method) set_input_as_output_from() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) (petpal.pipelines.steps_base.StepsAPI method) set_input_scan_properties() (petpal.preproc.motion_corr.MotionCorrect method) (petpal.preproc.motion_target.MotionTarget method) (petpal.preproc.register.RegisterBase method) (petpal.preproc.register.RegisterPet method) set_reference_img() (petpal.preproc.register.RegisterPet method) set_reg_kwargs() (petpal.preproc.motion_corr.MotionCorrect method) (petpal.preproc.register.RegisterBase method) (petpal.preproc.register.RegisterPet method) set_tac_extraction_func() (petpal.preproc.regional_tac_extraction.WriteRegionalTacs method) set_target_img() (petpal.preproc.motion_corr.MotionCorrect method) (petpal.preproc.register.RegisterBase method) (petpal.preproc.register.RegisterPet method) set_weights() (petpal.kinetic_modeling.tac_fitting.TACFitter method) (petpal.kinetic_modeling.tac_fitting.TACFitterWithoutBloodVolume method) set_ylim_min_to_zero() (petpal.visualizations.tac_plots.RegionalTacFigure method) (petpal.visualizations.tac_plots.TacFigure method) setup_linear_and_log_subplot() (petpal.visualizations.tac_plots.RegionalTacFigure method) (petpal.visualizations.tac_plots.TacFigure method) setup_linear_subplot() (petpal.visualizations.tac_plots.RegionalTacFigure method) (petpal.visualizations.tac_plots.TacFigure method) setup_log_subplot() (petpal.visualizations.tac_plots.RegionalTacFigure method) (petpal.visualizations.tac_plots.TacFigure method) shifted_tac() (petpal.utils.time_activity_curve.TimeActivityCurve method) SHORT_NAME (in module petpal.utils.useful_functions) sigma (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm property) solve_sgtm() (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm static method) start_in_mins (petpal.utils.scan_timing.ScanTimingInfo property) std (petpal.utils.stats.RegionalStats property) StepType (in module petpal.pipelines.steps_containers) sum_target() (petpal.preproc.motion_target.MotionTarget method) T tac (petpal.utils.time_activity_curve.TimeActivityCurve property) tac_dispersion() (petpal.utils.time_activity_curve.TimeActivityCurve static method) tac_uncertainty (petpal.kinetic_modeling.tac_uncertainty.TacUncertainty property) tac_werr (petpal.utils.time_activity_curve.TimeActivityCurve property) tacs_dir (petpal.kinetic_modeling.graphical_analysis.MultiTACGraphicalAnalysis property) (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis property) (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis property) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis property) (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep property) (petpal.pipelines.kinetic_modeling_steps.TACAnalysisStepMixin property) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep property) (petpal.utils.time_activity_curve.MultiTACAnalysisMixin property) (petpal.visualizations.tac_plots.RegionalTacFigure property) tacs_objects_dict (petpal.visualizations.tac_plots.RegionalTacFigure property) times_in_mins (petpal.utils.time_activity_curve.TimeActivityCurve property) to_tsv() (petpal.utils.time_activity_curve.TimeActivityCurve method) U unique_labels (petpal.preproc.symmetric_geometric_transfer_matrix.Sgtm property) update_dependencies() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) update_dependencies_for() (petpal.pipelines.pipelines.BIDS_Pipeline method) (petpal.pipelines.steps_containers.StepsPipeline method) update_frame() (petpal.visualizations.image_visualization.NiftiGifCreator method) update_props_with_formatted_fit_values() (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis method) V valid_model_names() (petpal.kinetic_modeling.tac_fitting.ConvTcmModelConfig class method) (petpal.kinetic_modeling.tac_fitting.FrameAvgdTcmModelConfig class method) (petpal.kinetic_modeling.tac_fitting.TcmModelConfig class method) validate_activity() (petpal.utils.time_activity_curve.TimeActivityCurve method) validate_analysis_inputs() (petpal.kinetic_modeling.rtm_analysis.MultiTACRTMAnalysis method) (petpal.kinetic_modeling.rtm_analysis.RTMAnalysis method) validate_bounds() (petpal.kinetic_modeling.fit_tac_with_rtms.FitTACWithRTMs method) validate_kwargs() (petpal.pipelines.kinetic_modeling_steps.GraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.ParametricGraphicalAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.RTMFittingAnalysisStep method) (petpal.pipelines.kinetic_modeling_steps.TCMFittingAnalysisStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep method) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep method) (petpal.pipelines.steps_base.ObjectBasedStep method) validate_kwargs_for_non_default_have_been_set() (petpal.pipelines.preproc_steps.ImagePairToArrayStep method) (petpal.pipelines.preproc_steps.ImageToImageStep method) (petpal.pipelines.preproc_steps.ResampleBloodTACStep method) (petpal.pipelines.preproc_steps.TACsFromSegmentationStep method) (petpal.pipelines.steps_base.FunctionBasedStep method) validate_mappings() (petpal.meta.label_maps.LabelMapLoader method) validate_method_inputs() (petpal.kinetic_modeling.fit_tac_with_rtms.FitTACWithRTMs method) validated_tcm() (petpal.kinetic_modeling.tac_fitting.MultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.TCMAnalysis static method) validated_tcm_function() (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis static method) validated_tcm_name() (petpal.kinetic_modeling.tac_fitting.FrameAveragedMultiTACTCMAnalysis static method) (petpal.kinetic_modeling.tac_fitting.FrameAveragedTCMAnalysis static method) verbose (petpal.pipelines.pca_guided_idif_steps.PCAGuidedFitIDIFStep property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedIDIFMixin property) (petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep property) W window_index_pairs() (petpal.preproc.motion_corr.MotionCorrect method) window_target_img() (petpal.preproc.motion_corr.MotionCorrect method) write_fig() (petpal.visualizations.tac_plots.RegionalTacFigure method) (petpal.visualizations.tac_plots.TacFigure method) write_gif() (petpal.visualizations.image_visualization.NiftiGifCreator method) write_tacs() (petpal.preproc.regional_tac_extraction.WriteRegionalTacs method)