2D-3D Fully convolutional neural networks for cardiac MR segmentation

In this paper, we develop a 2D and 3D segmentation pipelines for fully automated cardiac MR image segmentation using Deep Convolutional Neural Networks (CNN). Our models are trained end-to-end from scratch using the ACD Challenge 2017 dataset comprising of 100 studies, each containing Cardiac MR images in End Diastole and End Systole phase. We show that both our segmentation models achieve near state-of-the-art performance scores in terms of distance metrics and have convincing accuracy in terms of clinical parameters. A comparative analysis is provided by introducing a novel dice loss function and its combination with cross entropy loss. By exploring different network structures and comprehensive experiments, we discuss several key insights to obtain optimal model performance, which also is central to the theme of this challenge

Deep Learning Techniques for Automatic MRI Cardiac Multi-Structures Segmentation and Diagnosis: Is the Problem Solved?

Delineation of the left ventricular cavity, myocardium, and right ventricle from cardiac magnetic resonance images (multi-slice 2-D cine MRI) is a common clinical task to establish diagnosis. The automation of the corresponding tasks has thus been the subject of intense research over the past decades. In this paper, we introduce the "Automatic Cardiac Diagnosis Challenge" dataset (ACDC), the largest publicly available and fully annotated dataset for the purpose of cardiac MRI (CMR) assessment. The dataset contains data from 150 multi-equipments CMRI recordings with reference measurements and classification from two medical experts. The overarching objective of this paper is to measure how far state-of-the-art deep learning methods can go at assessing CMRI, i.e., segmenting the myocardium and the two ventricles as well as classifying pathologies. In the wake of the 2017 MICCAI-ACDC challenge, we report results from deep learning methods provided by nine research groups for the segmentation task and four groups for the classification task. Results show that the best methods faithfully reproduce the expert analysis, leading to a mean value of 0.97 correlation score for the automatic extraction of clinical indices and an accuracy of 0.96 for automatic diagnosis. These results clearly open the door to highly accurate and fully automatic analysis of cardiac CMRI. We also identify scenarios for which deep learning methods are still failing. Both the dataset and detailed results are publicly available online, while the platform will remain open for new submissions

Self-supervised skull reconstruction in brain CT images with decompressive craniectomy

Decompressive craniectomy (DC) is a common surgical procedure consisting of the removal of a portion of the skull that is performed after incidents such as stroke, traumatic brain injury (TBI) or other events that could result in acute subdural hemorrhage and/or increasing intracranial pressure. In these cases, CT scans are obtained to diagnose and assess injuries, or guide a certain therapy and intervention. We propose a deep learning based method to reconstruct the skull defect removed during DC performed after TBI from post-operative CT images. This reconstruction is useful in multiple scenarios, e.g. to support the creation of cranioplasty plates, accurate measurements of bone flap volume and total intracranial volume, important for studies that aim to relate later atrophy to patient outcome. We propose and compare alternative self-supervised methods where an encoder-decoder convolutional neural network (CNN) estimates the missing bone flap on post-operative CTs. The self-supervised learning strategy only requires images with complete skulls and avoids the need for annotated DC images. For evaluation, we employ real and simulated images with DC, comparing the results with other state-of-the-art approaches. The experiments show that the proposed model outperforms current manual methods, enabling reconstruction even in highly challenging cases where big skull defects have been removed during surgery