kinfitr : PET Kinetic Modelling using R

Overview

kinfitr is a package for PET Kinetic Modelling Using R. The main goal of this package is to equip PET modellers with great flexibility, while simultaneously making it easier to produce, present and share their results in a highly transparent manner using R and its ecosystem of tools for computational reproducibility.

Installation

This package is currently only available on GitHub. It can be downloaded as follows:

remotes::install_github("mathesong/kinfitr")

Citation

At present, there are two preprints out about kinfitr. Please cite at least one of these if you use kinfitr in your study.

An introduction to the package:

Matheson, G. J. (2019). Kinfitr: Reproducible PET Pharmacokinetic Modelling in R. bioRxiv: 755751. https://doi.org/10.1101/755751

A validation study compared against commercial software:

Tjerkaski, J., Cervenka, S., Farde, L., & Matheson, G. J. (2020). Kinfitr – an open source tool for reproducible PET modelling: Validation and evaluation of test-retest reliability. bioRxiv: 2020.02.20.957738. https://doi.org/10.1101/2020.02.20.957738

Background and Usage

I’ve written up a series of blog posts describing some PET modelling theory and demonstrating how the package can be used on my blog. These give a good general introduction to using the package.

• Part 1: PET Modelling Theory

• Part 2: Basics and Iteration using kinfitr

• Part 3: Finding tstar using kinfitr

• Part 4: Blood Processing using kinfitr

Implemented Models

Reference Region Models

• Simplified Reference Tissue Model (SRTM) (Lammertsma & Hume, 1996)

• Simplified Reference Tissue Model 2 (SRTM2) (Wu et al., 2002)

• Simplified Reference Tissue Model with Blood Volumes (SRTM-V) (Tomasi et al., 2008)

• Full Reference Tissue Model (FRTM) (Hume et al, 1991)

• Non-Invasive Logan Plot (Logan et al., 1996)

• Non-Invasive Multilinear Logan Plot (Turkheimer et al., 2003)

• Ichise Multilinear Reference Tissue Model 1 (MRTM1) (Ichise et al., 2003)

• Ichise Multilinear Reference Tissue Model 2 (MRTM2) (Ichise et al., 2003)

• Patlak Reference Tissue Model (Patlak & Blasberg, 1985)

Models Requiring Arterial Input

• One-Tissue Compartment Model

• Two-Tissue Compartment Model

• Two-Tissue Compartment Model with Irreversible Binding

• Two-Tissue Compartment Model with Macroparameter Parameterisation

• Logan Plot (Logan et al., 1990)

• Multilinear Logan Plot (Turkheimer et al., 2003)

• Ichise Multilinear Analysis 1 (MA1) (Ichise et al., 2002)

• Ichise Multilinear Analysis 2 (MA2) (Ichise et al., 2002)

• Patlak Plot (Patlak et al., 1983)

Other Models

• Simultaneous Estimation of Non-Displaceable Binding (SIME) (Ogden et al., 2015)

• Feng+1TC for Reference Tissue Modelling (Matheson et al., 2024)

• Spline fits for Reference TAC Denoising

Blood Data Preparation

The package also contains a large number of models and methods for preparing and modelling blood data to generate the metabolite-corrected arterial input function.

BIDS Data

The kinfitr package also contains functions for parsing PET BIDS data and extracting the relevant information from these files.

A containerised PET BIDS App called PETFit is under active development to allow users to perform PET kinetic modelling using PET preprocessing derivative data, which makes use of kinfitr functionality to do so.