Probabilistic Mapping and Automated Segmentation of Human Brainstem White Matter Bundles.

Brainstem white matter bundles are essential conduits for neural signaling involved in modulation of vital functions ranging from homeostasis to human consciousness. Their architecture forms the anatomic basis for brainstem connectomics, subcortical mesoscale circuit models, and deep brain navigation tools. However, their small size and complex morphology compared to cerebral white matter structures makes mapping and segmentation challenging in neuroimaging. This results in a near absence of automated brainstem white matter tracing methods. We leverage diffusion MRI tractography to create BrainStem Bundle Tool (BSBT), which segments eight key white matter bundles in the rostral brainstem. BSBT performs automated segmentation on a custom probabilistic fiber map generated from tractography with a convolutional neural network architecture tailored for detection of small structures. We demonstrate BSBTs robustness across diffusion MRI acquisition protocols through validation on healthy subject