Document Type

Conference Paper

Publication Date




Publication Title

Medical Imaging 2015: Image Guided Procedures, Robotic Interventions, and Modeling, Proceedings of SPIE Vol. 9415




94150I (1-10)

Conference Name

SPIE Medical Imaging, 21-26 February 2015, Orlando, FL


This paper presents a methodology for the digital formatting of a printed atlas of the brainstem and the delineation of cranial nerves from this digital atlas. It also describes on-going work on the 3D resampling and refinement of the 2D functional regions and nerve contours. 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, whereby our objective is to fill in each corresponding label, which is analogous to painting numbered regions in a paint-by-numbers kit. Any open contour typically coincides with a cranial nerve. This 2D phase is needed in order to produce densely labeled regions that can be stacked to produce 3D regions, as well as identifying the embedded paths and outer attachment points of cranial nerves. Cranial nerves are modeled using an explicit contour based technique called 1-Simplex. The relevance of cranial nerves modeling of this project is two-fold: i) this atlas will fill a void left by the brain segmentation communities, as no suitable digital atlas of the brainstem exists, and ii) this atlas is necessary to make explicit the attachment points of major nerves (except I and II) having a cranial origin.


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Original Publication Citation

Patel, N., Sultana, S., Rashid, T., Krusienski, D., & Audette, M. A. (2015). Application and histology-driven refinement of active contour models to functional region and nerve delineation: Towards a digital brainstem atlas. In Z. R. Yaniv & R. J. Webster, III (Eds.), Medical Imaging 2015: Image Guided Procedures, Robotic Interventions, and Modeling, Proceedings of SPIE Vol. 9415 (94150I). SPIE, Bellingham, WA.