NPBDREG: Uncertainty Assessment in Diffeomorphic Brain MRI Registration using a Non-parametric Bayesian Deep-Learning Based Approach

TL;DR

This paper introduces NPBDREG, a non-parametric Bayesian deep-learning framework for uncertainty estimation in brain MRI registration, improving accuracy, smoothness, and out-of-distribution data handling over existing methods.

Contribution

NPBDREG combines stochastic gradient Langevin dynamics with deep learning to provide more accurate and reliable uncertainty estimates in deformable image registration.

Findings

Better correlation of uncertainty with out-of-distribution data (r>0.95)

7.3% improvement in registration accuracy (Dice score 0.74 vs. 0.69)

18% reduction in registration folds (0.014 vs. 0.017)

Abstract

Quantification of uncertainty in deep-neural-networks (DNN) based image registration algorithms plays a critical role in the deployment of image registration algorithms for clinical applications such as surgical planning, intraoperative guidance, and longitudinal monitoring of disease progression or treatment efficacy as well as in research-oriented processing pipelines. Currently available approaches for uncertainty estimation in DNN-based image registration algorithms may result in sub-optimal clinical decision making due to potentially inaccurate estimation of the uncertainty of the registration stems for the assumed parametric distribution of the registration latent space. We introduce NPBDREG, a fully non-parametric Bayesian framework for uncertainty estimation in DNN-based deformable image registration by combining an Adam optimizer with stochastic gradient Langevin dynamics (SGLD) to characterize the underlying posterior distribution through posterior sampling. Thus, it has the potential to provide uncertainty estimates that are highly correlated with the presence of out of distribution data. We demonstrated the added-value of NPBDREG, compared to the baseline probabilistic VoxelMorph model (PrVXM), on brain MRI image registration using $390$ image pairs from four publicly available databases: MGH10, CMUC12, ISBR18 and LPBA40. The NPBDREG shows a better correlation of the predicted uncertainty with out-of-distribution data ($r>0.95$ vs. $r<0.5$) as well as a 7.3%improvement in the registration accuracy (Dice score, $0.74$ vs. $0.69$, $p \ll 0.01$), and 18% improvement in registration smoothness (percentage of folds in the deformation field, 0.014 vs. 0.017, $p \ll 0.01$). Finally, NPBDREG demonstrated a better generalization capability for data corrupted by a mixed structure noise (Dice score of $0.73$ vs. $0.69$, $p \ll 0.01$) compared to the baseline PrVXM approach.