Core Concepts
PyHySCO is a GPU-enabled EPI distortion correction tool that offers accurate and efficient correction of susceptibility artifacts in Echo-Planar Imaging.
Abstract
The content discusses the development of PyHySCO, a user-friendly EPI distortion correction tool implemented in PyTorch. It introduces the concept of reversed Gradient Polarity (RGP) methods for correcting susceptibility artifacts in Echo-Planar Imaging. The article details the algorithmic improvements in PyHySCO, such as its novel initialization scheme using 1D optimal transport. It also compares PyHySCO with other existing tools like TOPUP and HySCO, showcasing its accuracy and efficiency in distortion correction. The validation experiments using real and simulated data from the Human Connectome Project demonstrate PyHySCO's effectiveness at achieving high-quality corrections in seconds.
Introduction
- RGP methods are commonly used for correcting susceptibility artifacts in EPI.
- Existing post-processing tools do not fully leverage recent hardware advancements.
- PyHySCO aims to enable 3D RGP correction in seconds through GPU acceleration.
Methods
- Mathematical formulation based on physical forward model defined by Chang and Fitzpatrick (1992).
- Implementation of optimization algorithms like GN-PCG, ADMM, and LBFGS.
- Coding structure includes data storage, image model, correction model, regularization terms, Hessian computation, preconditioning, initialization methods, optimization process.
Results
- Validation datasets include real and simulated data from the Human Connectome Project.
- Comparison metrics include relative improvement of image distance, loss value, smoothness regularizer value.
- Optimal transport initialization scheme compared to multilevel initialization from HySCO.
Usage and Workflow
- Python script example demonstrates loading images, defining loss function, optimizer selection, field map initialization, optimization process.
Comparison of Optimizers on GPU and CPU
- Comparison of GN-PCG, ADMM, LBFGS optimizers on both CPU and GPU architectures.
Stats
PyHySCOは、Echo Planar Imaging(EPI)での感受性アーティファクトの歪みを効率的に修正するGPU対応ツールです。