Contour Models for Descriptive Patient-Specific Neuro-Anatomical Modeling: Towards a Digital Brainstem Atlas

This paper describes on-going work on the transposition to digital format of 2D images of a printed atlas of the brainstem. In MRI-based anatomical modeling for neurosurgery planning and simulation, the complexity of the functional anatomy entails a digital atlas approach, rather than less descriptive voxel or surface-based approaches. However, there is an insufficiency of descriptive digital atlases, in particular of the brainstem. Our approach proceeds from a series of numbered, contour-based sketches coinciding with slices of the brainstem featuring both closed and open contours. The closed contours coincide with functionally relevant regions, in which case our objective is to fill in each corresponding label, which is analogous to painting numbered regions in a paint-by-numbers kit. The open contours typically coincide with cranial nerve tracts as well as symbols representing the medullary pyramids. This 2D phase is needed in order to produce densely labeled regions that can be stacked to produce 3D regions, as well as identifying embedded paths and outer attachment points of cranial nerves. In future work, the stacked labeled regions will be resampled and refined probabilistically, through active contour and surface modeling based on MRI T1, T2 and tractographic data. The relevance to spine modeling of this project is two-fold: (i) this atlas will fill a void left by the spine and brain segmentation communities, as no digital atlas of the brainstem exist, and (ii) this atlas is necessary to make explicit the attachment points of major nerves having both cranial and spinal origin, specifically nerves X and XI, as well all the attachment points of cranial nerves other than I and II.