Deeply-Supervised CNN for Prostate Segmentation

Prostate segmentation from Magnetic Resonance (MR) images plays an important role in image guided interven- tion. However, the lack of clear boundary specifically at the apex and base, and huge variation of shape and texture between the images from different patients make the task very challenging. To overcome these problems, in this paper, we propose a deeply supervised convolutional neural network (CNN) utilizing the convolutional information to accurately segment the prostate from MR images. The proposed model can effectively detect the prostate region with additional deeply supervised layers compared with other approaches. Since some information will be abandoned after convolution, it is necessary to pass the features extracted from early stages to later stages. The experimental results show that significant segmentation accuracy improvement has been achieved by our proposed method compared to other reported approaches.Comment: Due to a crucial sign error in equation

Doctor of Philosophy in Computing

dissertationAn important area of medical imaging research is studying anatomical diffeomorphic shape changes and detecting their relationship to disease processes. For example, neurodegenerative disorders change the shape of the brain, thus identifying differences between the healthy control subjects and patients affected by these diseases can help with understanding the disease processes. Previous research proposed a variety of mathematical approaches for statistical analysis of geometrical brain structure in three-dimensional (3D) medical imaging, including atlas building, brain variability quantification, regression, etc. The critical component in these statistical models is that the geometrical structure is represented by transformations rather than the actual image data. Despite the fact that such statistical models effectively provide a way for analyzing shape variation, none of them have a truly probabilistic interpretation. This dissertation contributes a novel Bayesian framework of statistical shape analysis for generic manifold data and its application to shape variability and brain magnetic resonance imaging (MRI). After we carefully define the distributions on manifolds, we then build Bayesian models for analyzing the intrinsic variability of manifold data, involving the mean point, principal modes, and parameter estimation. Because there is no closed-form solution for Bayesian inference of these models on manifolds, we develop a Markov Chain Monte Carlo method to sample the hidden variables from the distribution. The main advantages of these Bayesian approaches are that they provide parameter estimation and automatic dimensionality reduction for analyzing generic manifold-valued data, such as diffeomorphisms. Modeling the mean point of a group of images in a Bayesian manner allows for learning the regularity parameter from data directly rather than having to set it manually, which eliminates the effort of cross validation for parameter selection. In population studies, our Bayesian model of principal modes analysis (1) automatically extracts a low-dimensional, second-order statistics of manifold data variability and (2) gives a better geometric data fit than nonprobabilistic models. To make this Bayesian framework computationally more efficient for high-dimensional diffeomorphisms, this dissertation presents an algorithm, FLASH (finite-dimensional Lie algebras for shooting), that hugely speeds up the diffeomorphic image registration. Instead of formulating diffeomorphisms in a continuous variational problem, Flash defines a completely new discrete reparameterization of diffeomorphisms in a low-dimensional bandlimited velocity space, which results in the Bayesian inference via sampling on the space of diffeomorphisms being more feasible in time. Our entire Bayesian framework in this dissertation is used for statistical analysis of shape data and brain MRIs. It has the potential to improve hypothesis testing, classification, and mixture models

Probabilistic prediction of Alzheimer’s disease from multimodal image data with Gaussian processes

Alzheimer’s disease, the most common form of dementia, is an extremely serious health problem, and one that will become even more so in the coming decades as the global population ages. This has led to a massive effort to develop both new treatments for the condition and new methods of diagnosis; in fact the two are intimately linked as future treatments will depend on earlier diagnosis, which in turn requires the development of biomarkers that can be used to identify and track the disease. This is made possible by studies such as the Alzheimer’s disease neuroimaging initiative which provides previously unimaginable quantities of imaging and other data freely to researchers. It is the task of early diagnosis that this thesis focuses on. We do so by borrowing modern machine learning techniques, and applying them to image data. In particular, we use Gaussian processes (GPs), a previously neglected tool, and show they can be used in place of the more widely used support vector machine (SVM). As combinations of complementary biomarkers have been shown to be more useful than the biomarkers are individually, we go on to show GPs can also be applied to integrate different types of image and non-image data, and thanks to their properties this improves results further than it does with SVMs. In the final two chapters, we also look at different ways to formulate both the prediction of conversion to Alzheimer’s disease as a machine learning problem and the way image data can be used to generate features for input as a machine learning algorithm. Both of these show how unconventional approaches may improve results. The result is an advance in the state-of-the-art for a very clinically important problem, which may prove useful in practice and show a direction of future research to further increase the usefulness of such method