Small Samples and Low-Cost Auto-Segmentation Method for Pelvic Organ-at-Risk Segmentation in Magnetic Resonance Images Using Deep-Learning

Abstract

In radiotherapy, magnetic resonance (MR) imaging has higher contrast of soft tissue, and no radiation compared with computed tomography (CT) scanning. Due to the high-cost of manual annotation, the deep-learning based automatic organ-at-risk (OAR) and target delineation algorithms are in high-demand, but the collecting of large amounts of high-quality annotated datasets remains difficulty. In this paper, we proposed a low-cost OAR segmentation method with semi-supervised annotation using small annotation samples of pelvic MR images. This study consisted of 94 patients diagnosed with rectal cancer from April 2018 to March 2021 at Peking University People's Hospital. We used 17 slices of MR images with annotation and 78 slices without annotation to train a deep-learning based segmentation model. The bladder, femoral heads, rectum and small intestine were selected as OAR. Semi-supervised method and ensemble learning were used for generating training set using small sample with annotation. Post-processing algorithm was used to correct the self-annotation data. Two of 14 annotation samples were set as test set. As for un-labeled images, 40 of them were set as semi-supervised annotation train set, the rest were test set. Besides, both 2D and 3D auto-segmentation networks were evaluated. The dice of bladder, femoral head left and right, rectum and small intestine between segmentation results and reference masks is 0.947, 0.983, 0.981, 0.900, 0.845 only using self-annotation and post-processing method of 2D segmentation model. And the dice of corresponding OAR is 0.871, 0.975, 0.975, 0.783, 0.724 using 3D segmentation network, 0.885,0.982, 0.982, 0.882, 0,814 using 2D segmentation network with supervised method (nnUNet). The 2D model outperformed 3D model with better segmentation performance, shorter inference time and fewer parameters. The results proved that we can train a multi-OAR segmentation model only using small annotation samples and other unlabeled samples. Ensemble learning and post-processing methods are necessary for semi-supervised data annotation. For anisotropy data, 2D model shows better performance than 3D models.