Left Atrial Segmentation in a Few Seconds Using Fully Convolutional Network and Transfer Learning

Abstract

In this paper, we propose a fast automatic method that segments left atrial cavity from 3D GE-MRIs without any manual assistance, using a fully convolutional network (FCN) and transfer learning. This FCN is the base network of VGG-16, pre-trained on ImageNet for natural image classification, and fine tuned with the training dataset of the MICCAI 2018 Atrial Segmentation Challenge. It relies on the “pseudo-3D” method published at ICIP 2017, which allows for segmenting objects from 2D color images which contain 3D information of MRI volumes. For each (Formula Presented) slice of the volume to segment, we consider three images, corresponding to the (Formula Presented), and (Formula Presented) slices of the original volume. These three gray-level 2D images are assembled to form a 2D RGB color image (one image per channel). This image is the input of the FCN to obtain a 2D segmentation of the (Formula Presented) slice. We process all slices, then stack the results to form the 3D output segmentation. With such a technique, the segmentation of the left atrial cavity on a 3D volume takes only a few seconds. We obtain a Dice score of 0.92 both on the training set in our experiments before the challenge, and on the test set of the challenge.