Symmetric diffeomorphic modeling of longtudinal structural MRI

This technology report describes the longitudinal registration approach that we intend to incorporate into SPM12. It essentially describes a group-wise intra-subject modeling framework, which combines diffeomorphic and rigid-body registration, incorporating a correction for the intensity inhomogeneity artifact usually seen in MRI data. Emphasis is placed on achieving internal consistency and accounting for many of the mathematical subtleties that most implementations overlook. The implementation was evaluated using examples from the OASIS Longitudinal MRI Data in Non-demented and Demented Older Adults

Robust and Optimal Methods for Geometric Sensor Data Alignment

Geometric sensor data alignment - the problem of finding the rigid transformation that correctly aligns two sets of sensor data without prior knowledge of how the data correspond - is a fundamental task in computer vision and robotics. It is inconvenient then that outliers and non-convexity are inherent to the problem and present significant challenges for alignment algorithms. Outliers are highly prevalent in sets of sensor data, particularly when the sets overlap incompletely. Despite this, many alignment objective functions are not robust to outliers, leading to erroneous alignments. In addition, alignment problems are highly non-convex, a property arising from the objective function and the transformation. While finding a local optimum may not be difficult, finding the global optimum is a hard optimisation problem. These key challenges have not been fully and jointly resolved in the existing literature, and so there is a need for robust and optimal solutions to alignment problems. Hence the objective of this thesis is to develop tractable algorithms for geometric sensor data alignment that are robust to outliers and not susceptible to spurious local optima. This thesis makes several significant contributions to the geometric alignment literature, founded on new insights into robust alignment and the geometry of transformations. Firstly, a novel discriminative sensor data representation is proposed that has better viewpoint invariance than generative models and is time and memory efficient without sacrificing model fidelity. Secondly, a novel local optimisation algorithm is developed for nD-nD geometric alignment under a robust distance measure. It manifests a wider region of convergence and a greater robustness to outliers and sampling artefacts than other local optimisation algorithms. Thirdly, the first optimal solution for 3D-3D geometric alignment with an inherently robust objective function is proposed. It outperforms other geometric alignment algorithms on challenging datasets due to its guaranteed optimality and outlier robustness, and has an efficient parallel implementation. Fourthly, the first optimal solution for 2D-3D geometric alignment with an inherently robust objective function is proposed. It outperforms existing approaches on challenging datasets, reliably finding the global optimum, and has an efficient parallel implementation. Finally, another optimal solution is developed for 2D-3D geometric alignment, using a robust surface alignment measure. Ultimately, robust and optimal methods, such as those in this thesis, are necessary to reliably find accurate solutions to geometric sensor data alignment problems

Automated Complexity-Sensitive Image Fusion

To construct a complete representation of a scene with environmental obstacles such as fog, smoke, darkness, or textural homogeneity, multisensor video streams captured in diferent modalities are considered. A computational method for automatically fusing multimodal image streams into a highly informative and unified stream is proposed. The method consists of the following steps: 1. Image registration is performed to align video frames in the visible band over time, adapting to the nonplanarity of the scene by automatically subdividing the image domain into regions approximating planar patches 2. Wavelet coefficients are computed for each of the input frames in each modality 3. Corresponding regions and points are compared using spatial and temporal information across various scales 4. Decision rules based on the results of multimodal image analysis are used to combine thewavelet coefficients from different modalities 5. The combined wavelet coefficients are inverted to produce an output frame containing useful information gathered from the available modalities Experiments show that the proposed system is capable of producing fused output containing the characteristics of color visible-spectrum imagery while adding information exclusive to infrared imagery, with attractive visual and informational properties

Generative shape and image analysis by combining Gaussian processes and MCMC sampling

Fully automatic analysis of faces is important for automatic access control, human computer interaction or for automatically evaluate surveillance videos. For humans it is easy to look at and interpret faces. Assigning attributes, moods or even intentions to the depicted person seem to happen without any difficulty. In contrast computers struggle even for simple questions and still fail to answer more demanding questions like: "Are these two persons looking at each other?" The interpretation of an image depicting a face is facilitated using a generative model for faces. Modeling the variability between persons, illumination, view angle or occlusions lead to a rich abstract representation. The model state encodes comprehensive information reducing the effort needed to solve a wide variety of tasks. However, to use a generative model, first the model needs to be built and secondly the model has to be adapted to a particular image. There exist many highly tuned algorithms for either of these steps. Most algorithms require more or less user input. These algorithms often lack robustness, full automation or wide applicability to different objects or data modalities. Our main contribution in this PhD-thesis is the presentation of a general, probabilistic framework to build and adapt generative models. Using the framework, we exploit information probabilistically in the domain it originates from, independent of the problem domain. The framework combines Gaussian processes and Data-Driven MCMC sampling. The generative models are built using the Gaussian process formulation. To adapt a model we use the Metropolis Hastings algorithm based on a propose-and-verify strategy. The framework consists of different well separated parts. Model building is separated from the adaptation. The adaptation is further separated into update proposals and a verification layer. This allows to adapt, exchange, remove or integrate individual parts without changes to other parts. The framework is presented in the context of facial data analysis. We introduce a new kernel exploiting the symmetry of faces and augment a learned generative model with additional flexibility. We show how a generative model is rigidly aligned, non-rigidly registered or adapted to 2d images with the same basic algorithm. We exploit information from 2d images to constrain 3d registration. We integrate directed proposal into sampling shifting the algorithm towards stochastic optimization. We show how to handle missing data by adapting the used likelihood model. We integrate a discriminative appearance model into the image likelihood model to handle occlusions. We demonstrate the wide applicability of our framework by solving also medical image analysis problems reusing the parts introduced for faces

A nexus of intrinsic dynamics underlies translocase priming

The cytoplasmic ATPase SecA and the membrane-embedded SecYEG channel assemble to form the Sec translocase. How this interaction primes and catalytically activates the translocase remains unclear. We show that priming exploits a nexus of intrinsic dynamics in SecA. Using atomistic simulations, smFRET, and HDX-MS, we reveal multiple dynamic islands that cross-talk with domain and quaternary motions. These dynamic elements are functionally important and conserved. Central to the nexus is a slender stem through which rotation of the preprotein clamp of SecA is biased by ATPase domain motions between open and closed clamping states. An H-bonded framework covering most of SecA enables multi-tier dynamics and conformational alterations with minimal energy input. As a result, cognate ligands select preexisting conformations and alter local dynamics to regulate catalytic activity and clamp motions. These events prime the translocase for high-affinity reception of non-folded preprotein clients. Dynamics nexuses are likely universal and essential in multi-liganded proteins.</p

Computational methods for the analysis of functional 4D-CT chest images.

Medical imaging is an important emerging technology that has been intensively used in the last few decades for disease diagnosis and monitoring as well as for the assessment of treatment effectiveness. Medical images provide a very large amount of valuable information that is too huge to be exploited by radiologists and physicians. Therefore, the design of computer-aided diagnostic (CAD) system, which can be used as an assistive tool for the medical community, is of a great importance. This dissertation deals with the development of a complete CAD system for lung cancer patients, which remains the leading cause of cancer-related death in the USA. In 2014, there were approximately 224,210 new cases of lung cancer and 159,260 related deaths. The process begins with the detection of lung cancer which is detected through the diagnosis of lung nodules (a manifestation of lung cancer). These nodules are approximately spherical regions of primarily high density tissue that are visible in computed tomography (CT) images of the lung. The treatment of these lung cancer nodules is complex, nearly 70% of lung cancer patients require radiation therapy as part of their treatment. Radiation-induced lung injury is a limiting toxicity that may decrease cure rates and increase morbidity and mortality treatment. By finding ways to accurately detect, at early stage, and hence prevent lung injury, it will have significant positive consequences for lung cancer patients. The ultimate goal of this dissertation is to develop a clinically usable CAD system that can improve the sensitivity and specificity of early detection of radiation-induced lung injury based on the hypotheses that radiated lung tissues may get affected and suffer decrease of their functionality as a side effect of radiation therapy treatment. These hypotheses have been validated by demonstrating that automatic segmentation of the lung regions and registration of consecutive respiratory phases to estimate their elasticity, ventilation, and texture features to provide discriminatory descriptors that can be used for early detection of radiation-induced lung injury. The proposed methodologies will lead to novel indexes for distinguishing normal/healthy and injured lung tissues in clinical decision-making. To achieve this goal, a CAD system for accurate detection of radiation-induced lung injury that requires three basic components has been developed. These components are the lung fields segmentation, lung registration, and features extraction and tissue classification. This dissertation starts with an exploration of the available medical imaging modalities to present the importance of medical imaging in today’s clinical applications. Secondly, the methodologies, challenges, and limitations of recent CAD systems for lung cancer detection are covered. This is followed by introducing an accurate segmentation methodology of the lung parenchyma with the focus of pathological lungs to extract the volume of interest (VOI) to be analyzed for potential existence of lung injuries stemmed from the radiation therapy. After the segmentation of the VOI, a lung registration framework is introduced to perform a crucial and important step that ensures the co-alignment of the intra-patient scans. This step eliminates the effects of orientation differences, motion, breathing, heart beats, and differences in scanning parameters to be able to accurately extract the functionality features for the lung fields. The developed registration framework also helps in the evaluation and gated control of the radiotherapy through the motion estimation analysis before and after the therapy dose. Finally, the radiation-induced lung injury is introduced, which combines the previous two medical image processing and analysis steps with the features estimation and classification step. This framework estimates and combines both texture and functional features. The texture features are modeled using the novel 7th-order Markov Gibbs random field (MGRF) model that has the ability to accurately models the texture of healthy and injured lung tissues through simultaneously accounting for both vertical and horizontal relative dependencies between voxel-wise signals. While the functionality features calculations are based on the calculated deformation fields, obtained from the 4D-CT lung registration, that maps lung voxels between successive CT scans in the respiratory cycle. These functionality features describe the ventilation, the air flow rate, of the lung tissues using the Jacobian of the deformation field and the tissues’ elasticity using the strain components calculated from the gradient of the deformation field. Finally, these features are combined in the classification model to detect the injured parts of the lung at an early stage and enables an earlier intervention

A review of point set registration: from pairwise registration to groupwise registration

Abstract: This paper presents a comprehensive literature review on point set registration. The state-of-the-art modeling methods and algorithms for point set registration are discussed and summarized. Special attention is paid to methods for pairwise registration and groupwise registration. Some of the most prominent representative methods are selected to conduct qualitative and quantitative experiments. From the experiments we have conducted on 2D and 3D data, CPD-GL pairwise registration algorithm [1] and JRMPC groupwise registration algorithm [2,3] seem to outperform their rivals both in accuracy and computational complexity. Furthermore, future research directions and avenues in the area are identified

Segmentation of Brain Magnetic Resonance Images (MRIs): A Review

Abstract MR imaging modality has assumed an important position in studying the characteristics of soft tissues. Generally, images acquired by using this modality are found to be affected by noise, partial volume effect (PVE) and intensity nonuniformity (INU). The presence of these factors degrades the quality of the image. As a result of which, it becomes hard to precisely distinguish between different neighboring regions constituting an image. To address this problem, various methods have been proposed. To study the nature of various proposed state-of-the-art medical image segmentation methods, a review was carried out. This paper presents a brief summary of this review and attempts to analyze the strength and weaknesses of the proposed methods. The review concludes that unfortunately, none of the proposed methods has been able to independently address the problem of precise segmentation in its entirety. The paper strongly favors the use of some module for restoring pixel intensity value along with a segmentation method to produce efficient results