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

Model Reduction of Muscle-Driven Tissue Models

Biomechanical simulations are a necessary tool for a proper understanding of biomechanics and hence are subject to intense research. One field that relies on this research is articulatory speech synthesis as it attempts to simulate the physics of the speech production process. Out of the many aspects involved, muscle driven tissue is one of the most important as it is required to simulate the deformable structures of the vocal tract. Modelling of muscle driven tissue requires continuum models of high complexity for the purpose of accuracy. On the other hand, time-efficient models are desirable in order to provide fast simulations which enable the user to test input parameters interactively. These requirements impose limitations on each other as the time-efficiency of a model is reduced with increasing complexity, hence techniques that can bridge the gap between these requirements are needed. This thesis attempts to bridge this gap through two major contributions. Model reduction techniques, that up until now have only been applied to inactive materials, have been implemented and tested for muscle driven tissue models. The implementation has been made in a general way to ensure that it can be used for biomechanical simulations in other fields than articulatory speech synthesis. In addition, the implementation has been made such that it can handle more advanced simulations than those investigated in this thesis. The simulations show acceptable but not ideal accuracy in both dynamic simulations and in measurements of equilibrium configurations. In addition, the reduced simulations using hyperreduction show good speedup for the more complex models investigated

Estimation of Fiber Orientations Using Neighborhood Information

Data from diffusion magnetic resonance imaging (dMRI) can be used to reconstruct fiber tracts, for example, in muscle and white matter. Estimation of fiber orientations (FOs) is a crucial step in the reconstruction process and these estimates can be corrupted by noise. In this paper, a new method called Fiber Orientation Reconstruction using Neighborhood Information (FORNI) is described and shown to reduce the effects of noise and improve FO estimation performance by incorporating spatial consistency. FORNI uses a fixed tensor basis to model the diffusion weighted signals, which has the advantage of providing an explicit relationship between the basis vectors and the FOs. FO spatial coherence is encouraged using weighted l1-norm regularization terms, which contain the interaction of directional information between neighbor voxels. Data fidelity is encouraged using a squared error between the observed and reconstructed diffusion weighted signals. After appropriate weighting of these competing objectives, the resulting objective function is minimized using a block coordinate descent algorithm, and a straightforward parallelization strategy is used to speed up processing. Experiments were performed on a digital crossing phantom, ex vivo tongue dMRI data, and in vivo brain dMRI data for both qualitative and quantitative evaluation. The results demonstrate that FORNI improves the quality of FO estimation over other state of the art algorithms.Comment: Journal paper accepted in Medical Image Analysis. 35 pages and 16 figure

Final Report to NSF of the Standards for Facial Animation Workshop

The human face is an important and complex communication channel. It is a very familiar and sensitive object of human perception. The facial animation field has increased greatly in the past few years as fast computer graphics workstations have made the modeling and real-time animation of hundreds of thousands of polygons affordable and almost commonplace. Many applications have been developed such as teleconferencing, surgery, information assistance systems, games, and entertainment. To solve these different problems, different approaches for both animation control and modeling have been developed

Multiparametric Magnetic Resonance Imaging Artificial Intelligence Pipeline for Oropharyngeal Cancer Radiotherapy Treatment Guidance

Oropharyngeal cancer (OPC) is a widespread disease and one of the few domestic cancers that is rising in incidence. Radiographic images are crucial for assessment of OPC and aid in radiotherapy (RT) treatment. However, RT planning with conventional imaging approaches requires operator-dependent tumor segmentation, which is the primary source of treatment error. Further, OPC expresses differential tumor/node mid-RT response (rapid response) rates, resulting in significant differences between planned and delivered RT dose. Finally, clinical outcomes for OPC patients can also be variable, which warrants the investigation of prognostic models. Multiparametric MRI (mpMRI) techniques that incorporate simultaneous anatomical and functional information coupled to artificial intelligence (AI) approaches could improve clinical decision support for OPC by providing immediately actionable clinical rationale for adaptive RT planning. If tumors could be reproducibly segmented, rapid response could be classified, and prognosis could be reliably determined, overall patient outcomes would be optimized to improve the therapeutic index as a function of more risk-adapted RT volumes. Consequently, there is an unmet need for automated and reproducible imaging which can simultaneously segment tumors and provide predictive value for actionable RT adaptation. This dissertation primarily seeks to explore and optimize image processing, tumor segmentation, and patient outcomes in OPC through a combination of advanced imaging techniques and AI algorithms. In the first specific aim of this dissertation, we develop and evaluate mpMRI pre-processing techniques for use in downstream segmentation, response prediction, and outcome prediction pipelines. Various MRI intensity standardization and registration approaches were systematically compared and benchmarked. Moreover, synthetic image algorithms were developed to decrease MRI scan time in an effort to optimize our AI pipelines. We demonstrated that proper intensity standardization and image registration can improve mpMRI quality for use in AI algorithms, and developed a novel method to decrease mpMRI acquisition time. Subsequently, in the second specific aim of this dissertation, we investigated underlying questions regarding the implementation of RT-related auto-segmentation. Firstly, we quantified interobserver variability for an unprecedented large number of observers for various radiotherapy structures in several disease sites (with a particular emphasis on OPC) using a novel crowdsourcing platform. We then trained an AI algorithm on a series of extant matched mpMRI datasets to segment OPC primary tumors. Moreover, we validated and compared our best model\u27s performance to clinical expert observers. We demonstrated that AI-based mpMRI OPC tumor auto-segmentation offers decreased variability and comparable accuracy to clinical experts, and certain mpMRI input channel combinations could further improve performance. Finally, in the third specific aim of this dissertation, we predicted OPC primary tumor mid-therapy (rapid) treatment response and prognostic outcomes. Using co-registered pre-therapy and mid-therapy primary tumor manual segmentations of OPC patients, we generated and characterized treatment sensitive and treatment resistant pre-RT sub-volumes. These sub-volumes were used to train an AI algorithm to predict individual voxel-wise treatment resistance. Additionally, we developed an AI algorithm to predict OPC patient progression free survival using pre-therapy imaging from an international data science competition (ranking 1st place), and then translated these approaches to mpMRI data. We demonstrated AI models could be used to predict rapid response and prognostic outcomes using pre-therapy imaging, which could help guide treatment adaptation, though further work is needed. In summary, the completion of these aims facilitates the development of an image-guided fully automated OPC clinical decision support tool. The resultant deliverables from this project will positively impact patients by enabling optimized therapeutic interventions in OPC. Future work should consider investigating additional imaging timepoints, imaging modalities, uncertainty quantification, perceptual and ethical considerations, and prospective studies for eventual clinical implementation. A dynamic version of this dissertation is publicly available and assigned a digital object identifier through Figshare (doi: 10.6084/m9.figshare.22141871)

Whole-body somatotopic maps in the cerebellum revealed with 7T fMRI

The cerebellum is known to contain a double somatotopic body representation. While the anterior lobe body map has shown a robust somatotopic organization in previous fMRI studies, the representations in the posterior lobe have been more difficult to observe and are less precisely characterized. In this study, participants went through a simple motor task asking them to move either the eyes (left-right guided saccades), tongue (left-right movement), thumbs, little fingers or toes (flexion). Using high spatial resolution fMRI data acquired at ultra-high field (7T), with special care taken to obtain sufficient B1 over the entire cerebellum and a cerebellar surface reconstruction facilitating visual inspection of the results, we were able to precisely map the somatotopic representations of these five distal body parts on both subject- and group-specific cerebellar surfaces. The anterior lobe (including lobule VI) showed a consistent and robust somatotopic gradient. Although less robust, the presence of such a gradient in the posterior lobe, from Crus II to lobule VIIIb, was also observed. Additionally, the eyes were also strongly represented in Crus I and the oculomotor vermis. Overall, crosstalk between the different body part representations was negligible. Taken together, these results show that multiple representations of distal body parts are present in the cerebellum, across many lobules, and they are organized in an orderly manner

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201