Anatomical landmark based registration of contrast enhanced T1-weighted MR images

In many problems involving multiple image analysis, an im- age registration step is required. One such problem appears in brain tumor imaging, where baseline and follow-up image volumes from a tu- mor patient are often to-be compared. Nature of the registration for a change detection problem in brain tumor growth analysis is usually rigid or affine. Contrast enhanced T1-weighted MR images are widely used in clinical practice for monitoring brain tumors. Over this modality, con- tours of the active tumor cells and whole tumor borders and margins are visually enhanced. In this study, a new technique to register serial contrast enhanced T1 weighted MR images is presented. The proposed fully-automated method is based on five anatomical landmarks: eye balls, nose, confluence of sagittal sinus, and apex of superior sagittal sinus. Af- ter extraction of anatomical landmarks from fixed and moving volumes, an affine transformation is estimated by minimizing the sum of squared distances between the landmark coordinates. Final result is refined with a surface registration, which is based on head masks confined to the sur- face of the scalp, as well as to a plane constructed from three of the extracted features. The overall registration is not intensity based, and it depends only on the invariant structures. Validation studies using both synthetically transformed MRI data, and real MRI scans, which included several markers over the head of the patient were performed. In addition, comparison studies against manual landmarks marked by a radiologist, as well as against the results obtained from a typical mutual information based method were carried out to demonstrate the effectiveness of the proposed method

Rheological Model for Wood

Wood as the most important natural and renewable building material plays an important role in the construction sector. Nevertheless, its hygroscopic character basically affects all related mechanical properties leading to degradation of material stiffness and strength over the service life. Accordingly, to attain reliable design of the timber structures, the influence of moisture evolution and the role of time- and moisture-dependent behaviors have to be taken into account. For this purpose, in the current study a 3D orthotropic elasto-plastic, visco-elastic, mechano-sorptive constitutive model for wood, with all material constants being defined as a function of moisture content, is presented. The corresponding numerical integration approach, with additive decomposition of the total strain is developed and implemented within the framework of the finite element method (FEM). Moreover to preserve a quadratic rate of asymptotic convergence the consistent tangent operator for the whole model is derived. Functionality and capability of the presented material model are evaluated by performing several numerical verification simulations of wood components under different combinations of mechanical loading and moisture variation. Additionally, the flexibility and universality of the introduced model to predict the mechanical behavior of different species are demonstrated by the analysis of a hybrid wood element. Furthermore, the proposed numerical approach is validated by comparisons of computational evaluations with experimental results.Comment: 37 pages, 13 figures, 10 table

Assessing the outcome of orthognathic surgery by three-dimensional soft tissue analysis

Studies of orthognathic surgery often focus on pre-surgical versus post-surgical changes in facial shape. In contrast, this study provides an innovative comparison between post-surgical and control shape. Forty orthognathic surgery patients were included, who underwent three different types of surgical correction: Le Fort I maxillary advancement, bilateral sagittal split mandibular advancement, and bimaxillary advancement surgery. Control facial images were captured from volunteers from local communities in Glasgow, with patterns of age, sex, and ethnic background that matched those of the surgical patients. Facial models were fitted and Procrustes registration and principal components analysis used to allow quantitative analysis, including the comparison of group mean shape and mean asymmetry. The primary characteristic of the difference in shape was found to be residual mandibular prognathism in the group of female patients who underwent Le Fort I maxillary advancement. Individual cases were assessed against this type of shape difference, using a quantitative scale to aid clinical audit. Analysis of the combined surgical groups provided strong evidence that surgery reduces asymmetry in some parts of the face such as the upper lip region. No evidence was found that mean asymmetry in post-surgical patients is greater than that in controls

Geometry Processing of Conventionally Produced Mouse Brain Slice Images

Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms for automatic registration and 3D reconstruction of conventionally produced mouse brain slices in a standardized atlas space. This is achieved first by constructing a virtual 3D mouse brain model from annotated slices of Allen Reference Atlas (ARA). Virtual re-slicing of the reconstructed model generates ARA-based slice images corresponding to the microscopic images of histological brain sections. These image pairs are aligned using a geometric approach through contour images. Histological artifacts in the microscopic images are detected and removed using Constrained Delaunay Triangulation before performing global alignment. Finally, non-linear registration is performed by solving Laplace's equation with Dirichlet boundary conditions. Our methods provide significant improvements over previously reported registration techniques for the tested slices in 3D space, especially on slices with significant histological artifacts. Further, as an application we count the number of neurons in various anatomical regions using a dataset of 51 microscopic slices from a single mouse brain. This work represents a significant contribution to this subfield of neuroscience as it provides tools to neuroanatomist for analyzing and processing histological data.Comment: 14 pages, 11 figure

Skull Flexure from Blast Waves: A Mechanism for Brain Injury with Implications for Helmet Design

Traumatic brain injury [TBI] has become a signature injury of current military conflicts, with debilitating, costly, and long-lasting effects. Although mechanisms by which head impacts cause TBI have been well-researched, the mechanisms by which blasts cause TBI are not understood. From numerical hydrodynamic simulations, we have discovered that non-lethal blasts can induce sufficient skull flexure to generate potentially damaging loads in the brain, even without a head impact. The possibility that this mechanism may contribute to TBI has implications for injury diagnosis and armor design.Comment: version in press, Physical Review Letters; 17 pages, 5 figures (includes supplementary material

Mathematical modeling of local perfusion in large distensible microvascular networks

Microvessels -blood vessels with diameter less than 200 microns- form large, intricate networks organized into arterioles, capillaries and venules. In these networks, the distribution of flow and pressure drop is a highly interlaced function of single vessel resistances and mutual vessel interactions. In this paper we propose a mathematical and computational model to study the behavior of microcirculatory networks subjected to different conditions. The network geometry is composed of a graph of connected straight cylinders, each one representing a vessel. The blood flow and pressure drop across the single vessel, further split into smaller elements, are related through a generalized Ohm's law featuring a conductivity parameter, function of the vessel cross section area and geometry, which undergo deformations under pressure loads. The membrane theory is used to describe the deformation of vessel lumina, tailored to the structure of thick-walled arterioles and thin-walled venules. In addition, since venules can possibly experience negative transmural pressures, a buckling model is also included to represent vessel collapse. The complete model including arterioles, capillaries and venules represents a nonlinear system of PDEs, which is approached numerically by finite element discretization and linearization techniques. We use the model to simulate flow in the microcirculation of the human eye retina, a terminal system with a single inlet and outlet. After a phase of validation against experimental measurements, we simulate the network response to different interstitial pressure values. Such a study is carried out both for global and localized variations of the interstitial pressure. In both cases, significant redistributions of the blood flow in the network arise, highlighting the importance of considering the single vessel behavior along with its position and connectivity in the network