Traumatic Brain Injury Segmentation using an Ensemble of Encoder-decoder Models

Abstract: The identification and segmentation of moderate-severe traumatic brain injury (TBI) lesions pose a significant challenge in neuroimaging. This difficulty arises from the extreme heterogeneity of these lesions, which vary in size, number, and laterality, thereby complicating downstream image processing tasks such as image registration and brain parcellation, reducing the analytical accuracy. Thus, developing methods for highly accurate segmentation of TBI lesions is essential for reliable neuroimaging analysis. This study aims to develop an effective automated segmentation pipeline to automatically detect and segment TBI lesions in T1-weighted MRI scans. We evaluate multiple approaches to achieve accurate segmentation of the TBI lesions. The core of our pipeline leverages various architectures within the nnUNet framework for initial segmentation, complemented by post-processing strategies to enhance evaluation metrics. Our final submission to the challenge achieved an accuracy of 0.8451, Dice score values of 0.4711 and 0.8514 for images with and without visible lesions, respectively, with an overall Dice score of 0.5973, ranking among the top-6 methods in the AIMS-TBI 2025 challenge. The Python implementation of our pipeline is publicly available.