3D Modelling of Brainstem in NEUROiD

Goyal, Priyanka and Raghavan, Mohan (2019) 3D Modelling of Brainstem in NEUROiD. Masters thesis, Indian institute of technology Hyderabad.

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Abstract

The brainstem is a part of the central nervous system which is responsible for the connection of the brain, spinal cord, and cerebellum together[16]. It houses many of the control centers for vital body functions, such as swallowing, breathing, and vasomotor control. Most of the cranial nerve nuclei are located in the brainstem, providing motor and sensory function to the facial muscles, tongue, pharynx, and larynx, as well as supplying the senses of taste, equilibrium, and hearing. It also has nuclei important for sympathetic and parasympathetic autonomic functions such as circulation, digestion, and metabolism. Many important neural structures and fiber tracts are concentrated in this small portion of the nervous system, and therefore even a very small lesion may have profound effects. Speech disorders, vestibular disturbance, abnormal consciousness, and respiratory disturbance are a few examples of possible outcomes of brainstem disorders caused by trauma, tumors, stroke, infections, and demyelination (multiple sclerosis)[17]. From many years people have been trying to study and understand the brainstem. They have come up with different ways to represent and model the brainstem on which they can work. It includes precise 2D anatomical atlases obtained from cadaveric brainstems [14]. Cadaveric models which can be a platform to perform anatomy based testing, or to get different SEZs, which can be helpful to plan surgeries[4]. Digital representations are also available for the brainstem. They include 3D atlases built with the help of different imaging techniques like CT, MRI, PET, tractography, Angiography, etc. which help to understand patient-specific pathology. These atlases also help in identification of the location of lesions[2, 6]. Many surgical planning platforms are available where data from CT, MRI, PET, angiography, etc. can be merged to get better 3D anatomical representations. They are also helpful to plan the surgery with a lot of available options like segmentation of anatomical structures, highlighting, etc. They can also act as a guide for surgery [9]. Computational models are also available which represent the physiology of the brainstem circuits and ultimately helps us to understand the respective etiology [10, 1, 7]. The above models represent either the anatomy, physiology or patient-specific clinical imaging. There is no common platform to represent all together. The brainstem model that we are building in the simulation environment NEUROiD will be the first step towards developing a platform with above-mentioned functionalities embedded in it. We will be able to populate different regions with neurons having different physiological properties. We will also be able to incorporate many functionalities like slicing a section or injecting current at a specific place etc. We will also try to incorporate system level simulations on this platform, so that understanding etiology will be possible. In the near future when the aforementioned functionalities are added to our platform, we can add a functionality to merge our model with patient-specific MRI, so that we will be able to understand patients pathology. The tractography images (where white tracts can be differentiated very well) can also be merged to our model and therefore can help us to plan surgeries with a best possible entry point and trajectory so that minimum damage happens to the surrounding tissues. With this, we can also design disease-specific models and therefore it can serve as a research tool too.

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