Development of microstructural and morphological cortical profiles in the neonatal brain

Interruptions to neurodevelopment during the perinatal period may have long-lasting consequences. However, to be able to investigate deviations in the foundation of proper connectivity and functional circuits, we need a measure of how this architecture evolves in the typically developing brain. To this end, in a cohort of 241 term-born infants, we used magnetic resonance imaging to estimate cortical profiles based on morphometry and microstructure over the perinatal period (37-44 weeks postmenstrual age, PMA). Using the covariance of these profiles as a measure of inter-areal network similarity (morphometric similarity networks; MSN), we clustered these networks into distinct modules. The resulting modules were consistent and symmetric, and corresponded to known functional distinctions, including sensory-motor, limbic, and association regions, and were spatially mapped onto known cytoarchitectonic tissue classes. Posterior regions became more morphometrically similar with increasing age, while peri-cingulate and medial temporal regions became more dissimilar. Network strength was associated with age: Within-network similarity increased over age suggesting emerging network distinction. These changes in cortical network architecture over an 8-week period are consistent with, and likely underpin, the highly dynamic processes occurring during this critical period. The resulting cortical profiles might provide normative reference to investigate atypical early brain development

Volumetric MRI Reconstruction from 2D Slices in the Presence of Motion

Despite recent advances in acquisition techniques and reconstruction algorithms, magnetic resonance imaging (MRI) remains challenging in the presence of motion. To mitigate this, ultra-fast two-dimensional (2D) MRI sequences are often used in clinical practice to acquire thick, low-resolution (LR) 2D slices to reduce in-plane motion. The resulting stacks of thick 2D slices typically provide high-quality visualizations when viewed in the in-plane direction. However, the low spatial resolution in the through-plane direction in combination with motion commonly occurring between individual slice acquisitions gives rise to stacks with overall limited geometric integrity. In further consequence, an accurate and reliable diagnosis may be compromised when using such motion-corrupted, thick-slice MRI data. This thesis presents methods to volumetrically reconstruct geometrically consistent, high-resolution (HR) three-dimensional (3D) images from motion-corrupted, possibly sparse, low-resolution 2D MR slices. It focuses on volumetric reconstructions techniques using inverse problem formulations applicable to a broad field of clinical applications in which associated motion patterns are inherently different, but the use of thick-slice MR data is current clinical practice. In particular, volumetric reconstruction frameworks are developed based on slice-to-volume registration with inter-slice transformation regularization and robust, complete-outlier rejection for the reconstruction step that can either avoid or efficiently deal with potential slice-misregistrations. Additionally, this thesis describes efficient Forward-Backward Splitting schemes for image registration for any combination of differentiable (not necessarily convex) similarity measure and convex (not necessarily smooth) regularization with a tractable proximal operator. Experiments are performed on fetal and upper abdominal MRI, and on historical, printed brain MR films associated with a uniquely long-term study dating back to the 1980s. The results demonstrate the broad applicability of the presented frameworks to achieve robust reconstructions with the potential to improve disease diagnosis and patient management in clinical practice

Robust similarity metrics for the registration of 3D multimodal medical images

In this paper, we develop data driven registration algorithms, relying on pixel similarity metrics, that enable an accurate rigid registration of dissimilar single or multimodal 2D/3D medical images . Gross dissimilarities are handled by considering similarity measures related to robust M-estimators . Fast stochastic multigrid optimization algorithms are used to minimize these similarity metrics . The proposed robust similarity metrics are compared to the most popular standard similarity metrics on real MRI/MRI and MRI/SPECT image pairs showing gross dissimilarities . A blinded evaluation of the algorithm was performed, using as gold standard a prospective, marker-based registration method, by participating in a registration evaluation project (Vanderbilt University) . Our robust similarity measures compare favourably with all standard (non robust) techniques .Le recalage non supervisé d'images médicales volumiques reste un problème difficile en raison de l'importante variabilité et des grandes différences d'information pouvant apparaître dans des séquences d'images de même modalité ou dans des couples d'images multimodales. Nous présentons dans cet article des méthodes robustes de recalage rigide d'images 2D et 3D monomodales et multimodales, reposant sur la minimisation de mesures de similarité inter-images. Les méthodes proposées s'appuient sur la théorie de l'estimation robuste et mettent en oeuvre des M-estimateurs associés à des techniques d'optimisation stochastique multigrilles rapides. Ces estimateurs robustes sont évalués à travers le recalage d'images médicales volumiques monomodales (IRM/IRM) et multimodales (IRM/TEMP). Ils sont comparés aux autres fonctions de similarité classiques, proposées dans la littérature. Les méthodes de recalage robustes ont, en particulier, été validées dans le cadre d'un protocole comparatif mis en place par l'Université de Vanderbilt. Elles sont actuellement utilisées en routine clinique et conduisent, tant pour les images de même modalité que pour les images multimodales à une précision sous-voxel, comparable aux meilleures méthodes actuelles. Elles permettent de plus de recaler des couples d'images sur lesquels les méthodes classiques échouent

A Pyramid Approach to Subpixel Registration Based on Intensity

We present an automatic sub-pixel registration algorithm that minimizes the mean square difference of intensities between a reference and a test data set, which can be either tri-dimensional (3-D) volumes or bi-dimensional (2-D) images. It uses spline processing, is based on a coarse-to-fine strategy (pyramid approach), and performs minimization according to a new variation of the iterative Marquardt-Levenberg algorithm for non-linear least-square optimization (MLA). The geometric deformation model is a global 3-D affine transformation, which one may restrict to the case of rigid-body motion (isometric scale, rotation and translation). It may also include a parameter to adjust for image contrast differences. We obtain excellent results for the registration of intra-modality Positron Emission Tomography (PET) and functional Magnetic Resonance Imaging (fMRI) data. We conclude that the multi-resolution refinement strategy is more robust than a comparable single-scale method, being less likely to get trapped into a false local optimum. In addition, it is also faster

Image Fusion and Axial Labeling of the Spine

In order to improve radiological diagnosis of back pain and spine disease, two new algorithms have been developed to aid the 75% of Canadians who will suffer from back pain in a given year. With the associated medical imaging required for many of these patients, there is a potential for improvement in both patient care and healthcare economics by increasing the accuracy and efficiency of spine diagnosis. A real-time spine image fusion system and an automatic vertebra/disc labeling system have been developed to address this. Both magnetic resonance (MR) images and computed tomography (CT) images are often acquired for patients. The MR image highlights soft tissue detail while the CT image highlights bone detail. It is desirable to present both modalities on a single fused image containing the clinically relevant detail. The fusion problem was encoded in an energy functional balancing three competing goals for the fused image: 1) similarity to the MR image, 2) similarity to the CT image and 3) smoothness (containing natural transitions). Graph-Cut and convex solutions have been developed. They have similar performance to each other and outperform other fusion methods from recent literature. The convex solution has real-time performance on modern graphics processing units, allowing for interactive control of the fused image. Clinical validation has been conducted on the convex solution based on 15 patient images. The fused images have been shown to increase confidence of diagnosis compared to unregistered MR and CT images, with no change in time for diagnosis based on readings from 5 radiologists. Spinal vertebrae serve as a reference for the location of surrounding tissues, but vertebrae have a very similar appearance to each other, making it time consume for radiologist to keep track of their locations. To automate this, an axial MR labeling algorithm was developed that runs in near real-time. Probability product kernels and fast integral images combined with simple geometric rules were used to classify pixels, slices and vertebrae. Evaluation was conducted on 32 lumbar spine images and 24 cervical spine images. The algorithm demonstrated 99% and 79% accuracy on the lumbar and cervical spine respectively

Development of Efficient Intensity Based Registration Techniques for Multi-modal Brain Images

Recent advances in medical imaging have resulted in the development of many imaging techniques that capture various aspects of the patients anatomy and metabolism. These are accomplished with image registration: the task of transforming images on a common anatomical coordinate space. Image registration is one of the important task for multi-modal brain images, which has paramount importance in clinical diagnosis, leads to treatment of brain diseases. In many other applications, image registration characterizes anatomical variability, to detect changes in disease state over time, and by mapping functional information into anatomical space. This thesis is focused to explore intensity-based registration techniques to accomplish precise information with accurate transformation for multi-modal brain images. In this view, we addressed mainly three important issues of image registration both in the rigid and non-rigid framework, i.e. i) information theoretic based similarity measure for alignment measurement, ii) free form deformation (FFD) based transformation, and iii) evolutionary technique based optimization of the cost function. Mutual information (MI) is a widely used information theoretic similarity measure criterion for multi-modal brain image registration. MI only dense the quantitative aspects of information based on the probability of events. For rustication of the information of events, qualitative aspect i.e. utility or saliency is a necessitate factor for consideration. In this work, a novel similarity measure is proposed, which incorporates the utility information into mutual Information, known as Enhanced Mutual Information(EMI).It is found that the maximum information gain using EMI is higher as compared to that of other state of arts. The utility or saliency employed in EMI is a scale invariant parameter, and hence it may fail to register in case of projective and perspective transformations. To overcome this bottleneck, salient region (SR) based Enhance Mutual Information (SR-EMI)is proposed, a new similarity measure for robust and accurate registration. The proposed SR-EMI based registration technique is robust to register the multi-modal brain images at a faster rate with better alignment

Automated Morphometric Characterization of the Cerebral Cortex for the Developing and Ageing Brain

Morphometric characterisation of the cerebral cortex can provide information about patterns of brain development and ageing and may be relevant for diagnosis and estimation of the progression of diseases such as Alzheimer's, Huntington's, and schizophrenia. Therefore, understanding and describing the differences between populations in terms of structural volume, shape and thickness is of critical importance. Methodologically, due to data quality, presence of noise, PV effects, limited resolution and pathological variability, the automated, robust and time-consistent estimation of morphometric features is still an unsolved problem. This thesis focuses on the development of tools for robust cross-sectional and longitudinal morphometric characterisation of the human cerebral cortex. It describes techniques for tissue segmentation, structural and morphometric characterisation, cross-sectional and longitudinally cortical thickness estimation from serial MRI images in both adults and neonates. Two new probabilistic brain tissue segmentation techniques are introduced in order to accurately and robustly segment the brain of elderly and neonatal subjects, even in the presence of marked pathology. Two other algorithms based on the concept of multi-atlas segmentation propagation and fusion are also introduced in order to parcelate the brain into its multiple composing structures with the highest possible segmentation accuracy. Finally, we explore the use of the Khalimsky cubic complex framework for the extraction of topologically correct thickness measurements from probabilistic segmentations without explicit parametrisation of the edge. A longitudinal extension of this method is also proposed. The work presented in this thesis has been extensively validated on elderly and neonatal data from several scanners, sequences and protocols. The proposed algorithms have also been successfully applied to breast and heart MRI, neck and colon CT and also to small animal imaging. All the algorithms presented in this thesis are available as part of the open-source package NiftySeg

Registration Methods for Quantitative Imaging

At the core of most image registration problems is determining a spatial transformation that relates the physical coordinates of two or more images. Registration methods have become ubiquitous in many quantitative imaging applications. They represent an essential step for many biomedical and bioengineering applications. For example, image registration is a necessary step for removing motion and distortion related artifacts in serial images, for studying the variation of biological tissue properties, such as shape and composition, across different populations, and many other applications. Here fully automatic intensity based methods for image registration are reviewed within a global energy minimization framework. A linear, shift-invariant, stochastic model for the image formation process is used to describe several important aspects of typical implementations of image registration methods. In particular, we show that due to the stochastic nature of the image formation process, most methods for automatic image registration produce answers biased towards `blurred' images. In addition we show how image approximation and interpolation procedures necessary to compute the registered images can have undesirable effects on subsequent quantitative image analysis methods. We describe the exact sources of such artifacts and propose methods through which these can be mitigated. The newly proposed methodology is tested using both simulated and real image data. Case studies using three-dimensional diffusion weighted magnetic resonance images, diffusion tensor images, and two-dimensional optical images are presented. Though the specific examples shown relate exclusively to the fields of biomedical imaging and biomedical engineering, the methods described are general and should be applicable to a wide variety of imaging problems