A Decoupled Uncertainty Model for MRI Segmentation Quality Estimation

Abstract: Quality control (QC) of MR images is essential to ensure that downstream analyses such as segmentation can be performed successfully. Currently, QC is predominantly performed visually and subjectively, at significant time and operator cost. We aim to automate the process using a probabilistic network that estimates segmentation uncertainty through a heteroscedastic noise model, providing a measure of task-specific quality. By augmenting training images with k-space artefacts, we propose a novel CNN architecture to decouple sources of uncertainty related to the task and different k-space artefacts in a self-supervised manner. This enables the prediction of separate uncertainties for different types of data degradation. While the uncertainty predictions reflect the presence and severity of artefacts, the network provides more robust and generalisable segmentation predictions given the quality of the data. We show that models trained with artefact augmentation provide informative measures of uncertainty on both simulated artefacts and problematic real-world images identified by human raters, both qualitatively and quantitatively in the form of error bars on volume measurements. Relating artefact uncertainty to segmentation Dice scores, we observe that our uncertainty predictions provide a better estimate of MRI quality from the point of view of the task (gray matter segmentation) compared to commonly used metrics of quality including signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), hence providing a real-time quality metric indicative of segmentation quality.