Subcortical Masks Generation in CT Images via Ensemble-Based Cross-Domain Label Transfer

Abstract: Subcortical segmentation in neuroimages plays an important role in understanding brain anatomy and facilitating computer-aided diagnosis of traumatic brain injuries and neurodegenerative disorders. However, training accurate automatic models requires large amounts of labelled data. Despite the availability of publicly available subcortical segmentation datasets for Magnetic Resonance Imaging (MRI), a significant gap exists for Computed Tomography (CT). This paper proposes an automatic ensemble framework to generate high-quality subcortical segmentation labels for CT scans by leveraging existing MRI-based models. We introduce a robust ensembling pipeline to integrate them and apply it to unannotated paired MRI-CT data, resulting in a comprehensive CT subcortical segmentation dataset. Extensive experiments on multiple public datasets demonstrate the superior performance of our proposed framework. Furthermore, using our generated CT dataset, we train segmentation models that achieve improved performance on related segmentation tasks. To facilitate future research, we make our source code, generated dataset, and trained models publicly available at https://github.com/SCSE-Biomedical-Computing-Group/CT-Subcortical-Segmentation, marking the first open-source release for CT subcortical segmentation to the best of our knowledge.