Combining General and Domain-Specific Pretext Tasks for Brain MR Image Segmentation

Tasneem Nasser, Susanne Schmid, Roberto Souza, Naser El-Sheimy

A key challenge in medical image analysis is the scarcity of large annotated datasets for specific populations and diseases. As deep learning models rely heavily on labeled data, effective transfer learning strategies are needed to reduce the dependence on manual annotations. Self-supervised learning has emerged as a promising approach for developing foundation models by enabling the learning of transferable feature representations from large-scale unlabeled medical imaging datasets. In this study, we investigate voxel-level brain age prediction as a domain-specific self-supervised pretext task and compare it with image inpainting, a widely used non-domain-specific alternative. We further propose a multitask self-supervised pretraining framework that jointly optimizes both objectives to learn complementary neuroimaging representations. The pretrained models are evaluated on three downstream magnetic resonance image segmentation tasks: multiple sclerosis lesion segmentation, ischemic stroke lesion segmentation, and cortical brain structure segmentation. Overall, the proposed multitask pretraining framework consistently outperformed the single-task pretrained models and training…