Automated olfactory bulb segmentation on high resolutional T2-weighted MRI

•First publicly available deep learning pipeline to segment the olfactory bulbs (OBs) in sub-millimeter T2-weighted whole-brain MRI.•Rigorous validation in the Rhineland Study - an ongoing large population-based cohort study - in terms of segmentation accuracy, stability and reliability of volume estimates, as well as sensitivity to replicate known OB volume associations (e.g. age effects).•Good generalizability to an unseen heterogeneous independent dataset (the Human Connectome Project).•Robustness even for individuals without apparent OBs, as can be encountered in large cohort studies. The neuroimage analysis community has neglected the automated segmentation of the olfactory bulb (OB) despite its crucial role in olfactory function. The lack of an automatic processing method for the OB can be explained by its challenging properties (small size, location, and poor visibility on traditional MRI scans). Nonetheless, recent advances in MRI acquisition techniques and resolution have allowed raters to generate more reliable manual annotations. Furthermore, the high accuracy of deep learning methods for solving semantic segmentation problems provides us with an option to reliably assess even small structures. In this work, we introduce a novel, fast, and fully automated deep learning pipeline to accurately segment OB tissue on sub-millimeter T2-weighted (T2w) whole-brain MR images. To this end, we designed a three-stage pipeline: (1) Localization of a region containing both OBs using FastSurferCNN, (2) Segmentation of OB tissue within the localized region through four independent AttFastSurferCNN - a novel deep learning architecture with a self-attention mechanism to improve modeling of contextual information, and (3) Ensemble of the predicted label maps. For this work, both OBs were manually annotated in a total of 620 T2w images for training (n=357) and testing. The OB pipeline exhibits high performance in terms of boundary delineation, OB localization, and volume estimation across a wide range of ages in 203 participants of the Rhineland Study (Dice Score (Dice): 0.852, Volume Similarity (VS): 0.910, and Average Hausdorff Distance (AVD): 0.215 mm). Moreover, it also generalizes to scans of an independent dataset never encountered during training, the Human Connectome Project (HCP), with different acquisition parameters and demographics, evaluated in 30 cases at the native 0.7 mm HCP resolution (Dice: 0.738, VS: 0.790, and AVD: 0.340 mm), and the default 0.8