Evaluating the Quality of Brain MRI Generators

TL;DR

This paper critically evaluates current metrics for assessing brain MRI generative models, proposing a new framework that emphasizes anatomical plausibility through reliable segmentation, leading to more meaningful quality assessments.

Contribution

It introduces a standardized evaluation framework for brain MRI generators that focuses on anatomical plausibility and segmentation reliability, addressing limitations of existing metrics.

Findings

Most existing metrics are sensitive to experimental setup.

Only half of the tested models produced high-quality MRIs.

Our framework's assessments align with qualitative evaluations.

Abstract

Deep learning models generating structural brain MRIs have the potential to significantly accelerate discovery of neuroscience studies. However, their use has been limited in part by the way their quality is evaluated. Most evaluations of generative models focus on metrics originally designed for natural images (such as structural similarity index and Frechet inception distance). As we show in a comparison of 6 state-of-the-art generative models trained and tested on over 3000 MRIs, these metrics are sensitive to the experimental setup and inadequately assess how well brain MRIs capture macrostructural properties of brain regions (i.e., anatomical plausibility). This shortcoming of the metrics results in inconclusive findings even when qualitative differences between the outputs of models are evident. We therefore propose a framework for evaluating models generating brain MRIs, which requires uniform processing of the real MRIs, standardizing the implementation of the models, and automatically segmenting the MRIs generated by the models. The segmentations are used for quantifying the plausibility of anatomy displayed in the MRIs. To ensure meaningful quantification, it is crucial that the segmentations are highly reliable. Our framework rigorously checks this reliability, a step often overlooked by prior work. Only 3 of the 6 generative models produced MRIs, of which at least 95% had highly reliable segmentations. More importantly, the assessment of each model by our framework is in line with qualitative assessments, reinforcing the validity of our approach.