3D PET/CT tumor segmentation based on nnU-Net with GCN refinement

Abstract

Abstract Objective. Whole-body positron emission tomography/computed tomography (PET/CT) scans are an important tool for diagnosing various malignancies (e.g. malignant melanoma, lymphoma, or lung cancer), and accurate segmentation of tumors is a key part of subsequent treatment. In recent years, convolutional neural network based segmentation methods have been extensively investigated. However, these methods often give inaccurate segmentation results, such as oversegmentation and undersegmentation. To address these issues, we propose a postprocessing method based on a graph convolutional network (GCN) to refine inaccurate segmentation results and improve the overall segmentation accuracy. Approach. First, nnU-Net is used as an initial segmentation framework, and the uncertainty in the segmentation results is analyzed. Certain and uncertain pixels are used to establish the nodes of a graph. Each node and its 6 neighbors form an edge, and 32 nodes are randomly selected as uncertain nodes to form edges. The highly uncertain nodes are used as the subsequent refinement targets. Second, the nnU-Net results of the certain nodes are used as labels to form a semisupervised graph network problem, and the uncertain part is optimized by training the GCN to improve the segmentation performance. This describes our proposed nnU-Net + GCN segmentation framework. Main results. We perform tumor segmentation experiments with the PET/CT dataset from the MICCIA2022 autoPET challenge. Among these data, 30 cases are randomly selected for testing, and the experimental results show that the false-positive rate is effectively reduced with nnU-Net + GCN refinement. In quantitative analysis, there is an improvement of 2.1% for the average Dice score, 6.4 for the 95% Hausdorff distance (HD95), and 1.7 for the average symmetric surface distance. Significance. The quantitative and qualitative evaluation results show that GCN postprocessing methods can effectively improve the tumor segmentation performance.