Segmentation, Survival Prediction, and Uncertainty Estimation of Gliomas from Multimodal 3D MRI Using Selective Kernel Networks

Abstract

AbstractSegmentation of gliomas into distinct sub-regions can help guide clinicians in tasks such as surgical planning, prognosis, and treatment response assessment. Manual delineation is time-consuming and prone to inter-rater variability. In this work, we propose a deep learning based automatic segmentation method that takes T1-pre, T1-post, T2, and FLAIR MRI as input and outputs a segmentation map of the sub-regions of interest (enhancing tumor (ET), whole tumor (WT), and tumor core (TC)). Our U-Net based architecture incorporates a modified selective kernel block to enable the network to adjust its receptive field via an attention mechanism, enabling more robust segmentation of gliomas of all appearances, shapes, and scales. Using this approach on the official BraTS 2020 testing set, we obtain Dice scores of .822, .889, and .834, and Hausdorff distances (95%) of 11.588, 4.812, and 21.984 for ET, WT, and TC, respectively. For prediction of overall survival, we extract deep features from the bottleneck layer of this network and train a Cox Proportional Hazards model, obtaining .495 accuracy. For uncertainty prediction, we achieve AUCs of .850, .914, and .854 for ET, WT, and TC, respectively, which earned us third place for this task.KeywordsCNNSegmentationU-NetBrain tumor