Head and Neck Tumor Segmentation on MRIs with Fast and Resource-Efficient Staged nnU-Nets

MRI-guided radiotherapy (RT) planning offers key advantages over conventional CT-based methods, including superior soft tissue contrast and the potential for daily adaptive RT due to the reduction of the radiation burden. In the Head and Neck (HN) region labor-intensive and time-consuming tumor segmentation still limits full utilization of MRI-guided adaptive RT. The HN Tumor Segmentation for MR-Guided Applications 2024 challenge (HNTS-MRG) aims to improve automatic tumor segmentation on MRI images by providing a dataset with reference annotations for the tasks of pre-RT and mid-RT planning. In this work, we present our approach for the HNTS-MRG challenge. Based on the insights of a thorough literature review we implemented a fast and resource-efficient two-stage segmentation method using the nnU-Net architecture with residual encoders as a backbone. In our two-stage approach we use the segmentation results of a first training round to guide the sampling process for a second refinement stage. For the pre-RT task, we achieved competitive results using only the first-stage nnU-Net. For the mid-RT task, we could significantly increase the segmentation performance of the basic first stage nnU-Net by utilizing the prior knowledge of the pre-RT plan as an additional input for the second stage refinement network. As team alpinists we achieved an aggregated Dice Coefficient of 80.97 for the pre-RT and 69.84 for the mid-RT task on the online test set of the challenge. Our code and trained model weights for the two-stage nnU-Net approach with residual encoders are available at https://github.com/elitap/hntsmrg24.