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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
Petpal
Cli
Cli Stats
Cli Stats
#
Run regional statistics on PET Images
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