Optical Flow-Guided Cine MRI Segmentation With Learned Corrections.

Abstract

In cardiac cine magnetic resonance imaging (MRI), the heart is repeatedly imaged at numerous time points during the cardiac cycle. Frequently, the temporal evolution of a certain region of interest such as the ventricles or the atria is highly relevant for clinical diagnosis. In this paper, we devise a novel approach that allows for an automatized propagation of an arbitrary region of interest (ROI) along the cardiac cycle from respective annotated ROIs provided by medical experts at two different points in time, most frequently at the end-systolic (ES) and the end-diastolic (ED) cardiac phases. At its core, a 3D TV- L1 -based optical flow algorithm computes the apparent motion of consecutive MRI images in forward and backward directions. Subsequently, the given terminal annotated masks are propagated by this bidirectional optical flow in 3D, which results, however, in improper initial estimates of the segmentation masks due to numerical inaccuracies. These initially propagated segmentation masks are then refined by a 3D U-Net-based convolutional neural network (CNN), which was trained to enforce consistency with the forward and backward warped masks using a novel loss function. Moreover, a penalization term in the loss function controls large deviations from the initial segmentation masks. This method is benchmarked both on a new dataset with annotated single ventricles containing patients with severe heart diseases and on a publicly available dataset with different annotated ROIs. We emphasize that our novel loss function enables fine-tuning the CNN on a single patient, thereby yielding state-of-the-art results along the complete cardiac cycle.