Multi-Material Mesh Representation of Anatomical Structures for Deep Brain Stimulation Planning

The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. The proposed method decomposes an ambiguous grid cube into a set of tetrahedral cells and uses novel polygon generation rules that produce 2-manifold and watertight surface meshes with good-quality triangles. These meshes, being watertight and 2-manifold, are geometrically correct, and therefore can be used to initialize tetrahedral meshes. The 2-manifold DC method has been extended into the multi-material domain. Due to its multi-material nature, multi-material surface meshes will contain non-manifold elements along material interfaces or shared boundaries. The proposed multi-material DC algorithm can (1) generate multi-material surface meshes where each material sub-mesh is a 2-manifold and watertight mesh, (2) preserve the non-manifold elements along the material interfaces, and (3) ensure that the material interface or shared boundary between materials is consistent. The proposed method is used to generate multi-material surface meshes of deep brain anatomical structures from a digital atlas of the basal ganglia and thalamus. Although deep brain anatomical structures can be labeled as functionally separate, they are in fact continuous tracts of soft tissue in close proximity to each other. The multi-material meshes generated by the proposed DC algorithm can accurately represent the closely-packed deep brain structures as a single mesh consisting of multiple material sub-meshes. Each sub-mesh represents a distinct functional structure of the brain. Printed and/or digital atlases are important tools for medical research and surgical intervention. While these atlases can provide guidance in identifying anatomical structures, they do not take into account the wide variations in the shape and size of anatomical structures that occur from patient to patient. Accurate, patient-specific representations are especially important for surgical interventions like deep brain stimulation, where even small inaccuracies can result in dangerous complications. The last part of this research effort extends the discrete deformable 2-simplex mesh into the multi-material domain where geometry-based internal forces and image-based external forces are used in the deformation process. This multi-material deformable framework is used to segment anatomical structures of the deep brain region from Magnetic Resonance (MR) data

Development of an Atlas-Based Segmentation of Cranial Nerves Using Shape-Aware Discrete Deformable Models for Neurosurgical Planning and Simulation

Twelve pairs of cranial nerves arise from the brain or brainstem and control our sensory functions such as vision, hearing, smell and taste as well as several motor functions to the head and neck including facial expressions and eye movement. Often, these cranial nerves are difficult to detect in MRI data, and thus represent problems in neurosurgery planning and simulation, due to their thin anatomical structure, in the face of low imaging resolution as well as image artifacts. As a result, they may be at risk in neurosurgical procedures around the skull base, which might have dire consequences such as the loss of eyesight or hearing and facial paralysis. Consequently, it is of great importance to clearly delineate cranial nerves in medical images for avoidance in the planning of neurosurgical procedures and for targeting in the treatment of cranial nerve disorders. In this research, we propose to develop a digital atlas methodology that will be used to segment the cranial nerves from patient image data. The atlas will be created from high-resolution MRI data based on a discrete deformable contour model called 1-Simplex mesh. Each of the cranial nerves will be modeled using its centerline and radius information where the centerline is estimated in a semi-automatic approach by finding a shortest path between two user-defined end points. The cranial nerve atlas is then made more robust by integrating a Statistical Shape Model so that the atlas can identify and segment nerves from images characterized by artifacts or low resolution. To the best of our knowledge, no such digital atlas methodology exists for segmenting nerves cranial nerves from MRI data. Therefore, our proposed system has important benefits to the neurosurgical community