PyPeT: A Python Perfusion Tool for Automated Quantitative Brain CT and MR Perfusion Analysis

TL;DR

PyPeT is an open-source Python tool that automates and customizes brain perfusion analysis from CT and MR data, providing reliable quantitative maps for cerebrovascular assessment.

Contribution

This work introduces PyPeT, a unified, modular, and open-source Python framework for processing brain perfusion data, with validation against commercial tools.

Findings

PyPeT produces high-quality perfusion maps with SSIM around 0.8.

PyPeT's outputs are comparable to FDA-approved commercial tools.

The tool is designed for accessibility, customizability, and low computational load.

Abstract

Computed tomography perfusion (CTP) and magnetic resonance perfusion (MRP) are widely used in acute ischemic stroke assessment and other cerebrovascular conditions to generate quantitative maps of cerebral hemodynamics. While commercial perfusion analysis software exists, it is often costly, closed source, and lacks customizability. This work introduces PyPeT, an openly available Python Perfusion Tool for head CTP and MRP processing. PyPeT is capable of producing cerebral blood flow (CBF), cerebral blood volume (CBV), mean transit time (MTT), time-to-peak (TTP), and time-to-maximum (Tmax) maps from raw four-dimensional perfusion data. PyPeT aims to make perfusion research as accessible and customizable as possible. This is achieved through a unified framework in which both CTP and MRP data can be processed, with a strong focus on modularity, low computational burden, and significant inline documentation. PyPeT's outputs can be validated through an extensive debug mode in which every step of the process is visualized. Additional validation was performed via visual and quantitative comparison with reference perfusion maps generated by three FDA-approved commercial perfusion tools and a research tool. These comparisons show a mean SSIM around 0.8 for all comparisons, indicating a good and stable correlation with FDA-approved tools. The code for PyPeT is openly available at our GitHub https://github.com/Marijn311/CT-and-MR-Perfusion-Tool