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PETPAL

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  • Petpal
    • Cli
      • Cli Graphical Analysis
        • _add_common_args
      • Cli Graphical Plots
      • Cli Idif
      • Cli Parametric Images
      • Cli Pib Processing
      • Cli Plot Tacs
      • Cli Preproc
        • _add_common_args
        • _generate_args
      • Cli Pvc
        • sgtm_cli_run
      • Cli Reference Tissue Models
        • add_common_args
        • parse_args
        • _generate_bounds
        • _pretty_print_results
      • Cli Stats
      • Cli Tac Fitting
        • add_common_io_args
        • add_common_analysis_args
        • add_common_print_args
        • _generate_args
        • _generate_bounds
        • fit_props_printer
      • Cli Tac Interpolation
        • _safe_write_tac
        • _print_tac_to_screen
      • Cli Vat Processing
        • infer_group
        • rename_subs
        • vat_protocol
    • Input Function
      • Blood Input
        • BloodInputFunction
        • extract_blood_input_function_from_csv
        • extract_blood_input_function_times_from_csv
        • extract_blood_input_function_activity_from_csv
        • resample_blood_data_on_scanner_times
        • read_plasma_glucose_concentration
      • Idif Necktangle
        • single_threshold_idif_from_4d_pet_with_necktangle
        • average_across_4d_frames
        • get_frame_time_midpoints
        • load_fslmeants_to_numpy_3d
        • double_threshold_idif_from_4d_pet_necktangle
      • Pca Guided Idif
        • PCAGuidedIdifBase
        • PCAGuidedTopVoxelsIDIF
        • PCAGuidedIdifFitterBase
        • PCAGuidedIdifFitter
    • Io
      • Image
        • ImageLoader
      • Table
        • TableSaver
        • get_tabular_separator
    • Kinetic Modeling
      • Fit Tac With Rtms
        • FitTACWithRTMs
        • get_rtm_method
        • get_rtm_kwargs
        • get_rtm_output_size
      • Graphical Analysis
        • GraphicalAnalysis
        • MultiTACGraphicalAnalysis
        • _line_fitting_make_rhs_matrix_from_xdata
        • fit_line_to_data_using_lls
        • fit_line_to_data_using_lls_with_rsquared
        • linear_least_squares_fit_with_stats
        • cumulative_trapezoidal_integral
        • calculate_patlak_x
        • get_index_from_threshold
        • patlak_analysis
        • patlak_analysis_with_rsquared
        • logan_analysis
        • logan_analysis_with_rsquared
        • logan_ref_region_analysis
        • logan_ref_region_analysis_with_rsquared
        • alternative_logan_analysis
        • alternative_logan_analysis_with_rsquared
        • get_graphical_analysis_method
        • get_graphical_analysis_method_with_rsquared
        • km_multifit_analysis_to_tsv
        • km_multifit_analysis_to_jsons
      • Parametric Images
        • ReferenceTissueParametricImage
        • GraphicalAnalysisParametricImage
        • apply_linearized_analysis_to_all_voxels
        • parametric_refregion_analysis
        • generate_parametric_images_with_graphical_method
        • apply_mrtm2_to_all_voxels
        • apply_rtm2_to_all_voxels
        • generate_cmrglc_parametric_image_from_ki_image
      • Reference Tissue Models
        • calc_srtm_tac
        • _calc_simplified_frtm_tac
        • _calc_frtm_params_from_kinetic_params
        • calc_frtm_tac
        • fit_srtm_to_tac
        • fit_srtm2_to_tac
        • fit_srtm_to_tac_with_bounds
        • fit_srtm2_to_tac_with_bounds
        • fit_frtm_to_tac
        • fit_frtm2_to_tac
        • fit_frtm_to_tac_with_bounds
        • fit_frtm2_to_tac_with_bounds
        • fit_mrtm_original_to_tac
        • fit_mrtm_2003_to_tac
        • fit_mrtm2_2003_to_tac
        • calc_bp_from_mrtm_original_fit
        • calc_bp_from_mrtm_2003_fit
        • calc_bp_from_mrtm2_2003_fit
        • calc_k2prime_from_mrtm_original_fit
        • calc_k2prime_from_mrtm_2003_fit
      • Rtm Analysis
        • RTMAnalysis
        • MultiTACRTMAnalysis
      • Tac Fitting
        • TcmModelConfig
        • ConvTcmModelConfig
        • TACFitter
        • TACFitterWithoutBloodVolume
        • TCMAnalysis
        • MultiTACTCMAnalysis
        • FrameAvgdTcmModelConfig
        • FrameAveragedTACFitter
        • FrameAveragedTCMAnalysis
        • FrameAveragedMultiTACTCMAnalysis
        • _get_fitting_params_for_tcm_func
        • _get_number_of_fit_params_for_tcm_func
      • Tac Interpolation
        • EvenlyInterpolate
        • EvenlyInterpolateWithMax
      • Tac Uncertainty
        • TacUncertainty
      • Tcms As Convolutions
        • calc_convolution_with_check
        • discrete_convolution_with_exponential
        • response_function_1tcm_c1
        • response_function_2tcm_with_k4zero_c1
        • response_function_2tcm_with_k4zero_c2
        • response_function_serial_2tcm_c1
        • response_function_serial_2tcm_c2
        • gen_tac_1tcm_cpet_from_tac
        • generate_tac_2tcm_with_k4zero_c1_from_tac
        • generate_tac_2tcm_with_k4zero_c2_from_tac
        • gen_tac_2tcm_with_k4zero_cpet_from_tac
        • generate_tac_serial_2tcm_c1_from_tac
        • generate_tac_serial_2tcm_c2_from_tac
        • gen_tac_2tcm_cpet_from_tac
        • model_serial_1tcm_frame_avgd
        • model_serial_2tcm_frame_avgd
    • Meta
      • Auto Cli
        • ParseKwargs
        • PetpalLogging
        • camel_to_kebab_case
        • args_kwargs_to_dictionary
        • type_identifier
        • auto_cli
      • Label Maps
        • LabelMapLoader
    • Pipelines
      • Kinetic Modeling Steps
        • TACAnalysisStepMixin
        • GraphicalAnalysisStep
        • TCMFittingAnalysisStep
        • RTMFittingAnalysisStep
        • ParametricGraphicalAnalysisStep
      • Pca Guided Idif Steps
        • PCAGuidedIDIFMixin
        • PCAGuidedFitIDIFStep
        • PCAGuidedTopVoxelsIDIFStep
      • Pipelines
        • BIDSyPathsForRawData
        • BIDSyPathsForPipelines
        • BIDS_Pipeline
      • Preproc Steps
        • TACsFromSegmentationStep
        • ResampleBloodTACStep
        • ImageToImageStep
        • ImagePairToArrayStep
      • Steps Base
        • ArgsDict
        • StepsAPI
        • FunctionBasedStep
        • ObjectBasedStep
      • Steps Containers
        • StepsContainer
        • StepsPipeline
    • Preproc
      • Brain Mask Pet
        • brain_mask_pet
      • Decay Correction
        • DecayCorrect
        • DecayFix
        • undo_decay_correction
        • decay_correct
        • calculate_frame_decay_factor
        • scale_frames
      • Image Operations 4d
        • SimpleAutoImageCropper
        • stitch_broken_scans
        • crop_image
        • rescale_image
        • extract_mean_roi_tac_from_nifti_using_segmentation
        • threshold
        • binarize_image_with_threshold
        • gauss_blur
        • roi_tac
      • Motion Corr
        • MotionCorrect
        • windowed_motion_corr_to_target
      • Motion Target
        • MotionTarget
        • determine_motion_target
      • Partial Volume Corrections
        • PetPvc
      • Regional Tac Extraction
        • WriteRegionalTacs
        • extract_roi_voxel_tacs_from_image_using_mask
        • apply_mask_4d
        • voxel_average_w_uncertainty
        • write_tacs
        • roi_tac
      • Register
        • RegisterBase
        • RegisterPet
        • register_pet_to_pet
        • register_pet
        • warp_pet_to_atlas
        • apply_xfm_ants
        • apply_xfm_fsl
        • resample_nii_4dfp
      • Segmentation Tools
        • combine_regions_as_mask
        • segmentations_merge
        • binarize
        • parcellate_right_left
        • replace_probabilistic_region
        • resample_segmentation
        • vat_wm_ref_region
        • eroded_wm_segmentation
        • vat_wm_region_merge
        • gw_segmentation
        • subcortical_mask
        • calc_vesselness_measure_image
        • calc_vesselness_mask_from_quantiled_vesselness
        • unique_segmentation_labels
        • seg_crop_to_pet_fov
      • Standard Uptake Value
        • weighted_sum_for_suv
        • suv
        • suvr
      • Symmetric Geometric Transfer Matrix
        • Sgtm
    • Utils
      • Bids Utils
        • add_description_to_bids_path
        • validate_filepath_as_bids
        • validate_directory_as_bids
        • parse_path_to_get_subject_and_session_id
        • snake_to_camel_case
        • gen_bids_like_filename
        • gen_bids_like_dir_path
        • gen_bids_like_filepath
      • Constants
      • Data Driven Image Analyses
        • temporal_pca_analysis_of_image_over_mask
        • extract_temporal_pca_components_of_image_over_mask
        • extract_temporal_pca_projection_of_image_over_mask
        • extract_temporal_pca_quantile_thresholded_tacs_of_image_using_mask
        • generate_temporal_pca_quantile_threshold_tacs_of_image_over_mask
        • _generate_quantiled_multi_tacs_header
        • _gen_reshaped_quantiled_tacs
      • Decorators
        • ANTsImageToANTsImage
      • Dimension
        • gen_nd_image_based_on_image_list
        • timeseries_from_img_list
        • gen_3d_img_from_timeseries
        • get_frame_from_timeseries
        • check_physical_space_for_ants_image_pair
      • Image Io
        • ImageIO
        • write_dict_to_json
        • gen_meta_data_filepath_for_nifti
        • safe_load_meta
        • load_metadata_for_nifti_with_same_filename
        • flatten_metadata
        • safe_copy_meta
        • get_half_life_from_radionuclide
        • get_half_life_from_meta
        • get_half_life_from_nifti
        • read_label_map_tsv
        • safe_load_4dpet_nifti
        • validate_two_images_same_dimensions
        • infer_sub_ses_from_tac_path
        • km_regional_fits_to_tsv
      • Math Lib
        • weighted_sum_computation
        • weighted_sum_computation_over_index_window
        • gauss_blur_computation
      • Metadata
        • BidsMetadataMender
      • Scan Timing
        • ScanTimingInfo
        • get_window_index_pairs_from_durations
        • get_window_index_pairs_for_image
        • calculate_frame_reference_time
      • Stats
        • RegionalStats
        • mean_value_in_region
      • Testing Utils
        • generate_random_parameter_samples
        • add_gaussian_noise_to_tac_based_on_max
        • scatter_with_regression_figure
        • bland_atlman_figure
        • ratio_bland_atlman_figure
      • Time Activity Curve
        • TimeActivityCurve
        • MultiTACAnalysisMixin
        • safe_load_tac
        • safe_write_tac
        • get_frame_index_pairs_from_fine_times
        • get_frame_averaged_tac_vals
      • Useful Functions
        • make_path
        • abbreviate_region
        • build_label_map
        • weighted_series_sum
        • weighted_series_sum_over_window_indices
        • read_plasma_glucose_concentration
        • convert_ctab_to_dseg
        • capitalize_first_char_of_str
        • str_to_camel_case
        • nearest_frame_to_timepoint
        • get_average_of_timeseries
        • coerce_outpath_extension
    • Visualizations
      • Graphical Plots
        • GraphicalAnalysisPlot
        • PatlakPlot
        • LoganPlot
        • AltLoganPlot
        • Plot
      • Image Visualization
        • NiftiGifCreator
      • Qc Plots
        • motion_plot
      • Tac Plots
        • TacFigure
        • RegionalTacFigure
  • API Reference

API Reference#

  • Petpal
    • Cli
    • Input Function
    • Io
    • Kinetic Modeling
    • Meta
    • Pipelines
    • Preproc
    • Utils
    • Visualizations

This page contains auto-generated API reference documentation [1].

[1]

Created with sphinx-autoapi

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