White Matter Structural Connectivity is Associated with Sensorimotor Function in Stroke Survivors

Purpose Diffusion tensor imaging (DTI) provides functionally relevant information about white matter structure. Local anatomical connectivity information combined with fractional anisotropy (FA) and mean diffusivity (MD) may predict functional outcomes in stroke survivors. Imaging methods for predicting functional outcomes in stroke survivors are not well established. This work uses DTI to objectively assess the effects of a stroke lesion on white matter structure and sensorimotor function. Methods A voxel-based approach is introduced to assess a stroke lesion\u27s global impact on motor function. Anatomical T1-weighted and diffusion tensor images of the brain were acquired for nineteen subjects (10 post-stroke and 9 age-matched controls). A manually selected volume of interest was used to alleviate the effects of stroke lesions on image registration. Images from all subjects were registered to the images of the control subject that was anatomically closest to Talairach space. Each subject\u27s transformed image was uniformly seeded for DTI tractography. Each seed was inversely transformed into the individual subject space, where DTI tractography was conducted and then the results were transformed back to the reference space. A voxel-wise connectivity matrix was constructed from the fibers, which was then used to calculate the number of directly and indirectly connected neighbors of each voxel. A novel voxel-wise indirect structural connectivity (VISC) index was computed as the average number of direct connections to a voxel\u27s indirect neighbors. Voxel-based analyses (VBA) were performed to compare VISC, FA, and MD for the detection of lesion-induced changes in sensorimotor function. For each voxel, a t-value was computed from the differences between each stroke brain and the 9 controls. A series of linear regressions was performed between Fugl-Meyer (FM) assessment scores of sensorimotor impairment and each DTI metric\u27s log number of voxels that differed from the control group. Results Correlation between the logarithm of the number of significant voxels in the ipsilesional hemisphere and total Fugl-Meyer score was moderate for MD (R2 = 0.512), and greater for VISC (R2 = 0.796) and FA (R2 = 0.674). The slopes of FA (p = 0.0036), VISC (p = 0.0005), and MD (p = 0.0199) versus the total FM score were significant. However, these correlations were driven by the upper extremity motor component of the FM score (VISC: R2 = 0.879) with little influence of the lower extremity motor component (FA: R2 = 0.177). Conclusion The results suggest that a voxel-wise metric based on DTI tractography can predict upper extremity sensorimotor function of stroke survivors, and that supraspinal intraconnectivity may have a less dominant role in lower extremity function

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

Geodesic boundary value problems with symmetry

This paper shows how left and right actions of Lie groups on a manifold may be used to complement one another in a variational reformulation of optimal control problems equivalently as geodesic boundary value problems with symmetry. We prove an equivalence theorem to this effect and illustrate it with several examples. In finite-dimensions, we discuss geodesic flows on the Lie groups SO(3) and SE(3) under the left and right actions of their respective Lie algebras. In an infinite-dimensional example, we discuss optimal large-deformation matching of one closed curve to another embedded in the same plane. In the curve-matching example, the manifold \Emb(S^1, \mathbb{R}^2) comprises the space of closed curves $S^1$ embedded in the plane $\mathbb{R}^2$. The diffeomorphic left action \Diff(\mathbb{R}^2) deforms the curve by a smooth invertible time-dependent transformation of the coordinate system in which it is embedded, while leaving the parameterisation of the curve invariant. The diffeomorphic right action \Diff(S^1) corresponds to a smooth invertible reparameterisation of the $S^1$ domain coordinates of the curve. As we show, this right action unlocks an important degree of freedom for geodesically matching the curve shapes using an equivalent fixed boundary value problem, without being constrained to match corresponding points along the template and target curves at the endpoint in time.Comment: First version -- comments welcome

Editing faces in videos

Editing faces in movies is of interest in the special effects industry. We aim at producing effects such as the addition of accessories interacting correctly with the face or replacing the face of a stuntman with the face of the main actor. The system introduced in this thesis is based on a 3D generative face model. Using a 3D model makes it possible to edit the face in the semantic space of pose, expression, and identity instead of pixel space, and due to its 3D nature allows a modelling of the light interaction. In our system we first reconstruct the 3D face, which is deforming because of expressions and speech, the lighting, and the camera in all frames of a monocular input video. The face is then edited by substituting expressions or identities with those of another video sequence or by adding virtual objects into the scene. The manipulated 3D scene is rendered back into the original video, correctly simulating the interaction of the light with the deformed face and virtual objects. We describe all steps necessary to build and apply the system. This includes registration of training faces to learn a generative face model, semi-automatic annotation of the input video, fitting of the face model to the input video, editing of the fit, and rendering of the resulting scene. While describing the application we introduce a host of new methods, each of which is of interest on its own. We start with a new method to register 3D face scans to use as training data for the face model. For video preprocessing a new interest point tracking and 2D Active Appearance Model fitting technique is proposed. For robust fitting we introduce background modelling, model-based stereo techniques, and a more accurate light model

Intervertebral Disc Structure and Mechanical Function Under Physiological Loading Quantified Non-invasively Utilizing MRI and Image Registration

The intervertebral discs (IVD) functions to permit motion, distribute load, and dissipate energy in the spine. It performs these functions through its heterogeneous structural organization and biochemical composition consisting of several tissue substructures: the central gelatinous nucleus pulposus (NP), the surrounding fiber reinforced layered annulus fibrosus (AF), and the cartilaginous endplates (CEP) that are positioned between the NP and vertebral endplates. Each tissue contributes individually to overall disc mechanics and by interacting with adjacent tissues. Disruption of the disc\u27s tissues through aging, degeneration, or tear will not only alter the affected tissue mechanical properties, but also the mechanical behavior of adjacent tissues and, ultimately, overall disc segment function. Thus, there is a need to measure disc tissue and segment mechanics in the intact disc so that interactions between substructures are not disrupted. Such measurements would be valuable to study mechanisms of disc function and degeneration, and develop and evaluate surgical procedures and therapeutic implants. The objectives of this study were to develop, validate, and apply methods to visualize and quantify IVD substructure geometry and track internal deformations for intact human discs under axial compression. The CEP and AF were visualized through MRI parameter mapping and image sequence optimization for ideal contrast. High-resolution images enabled geometric measurements. Axial compression was performed using a custom-built loading device that permitted long relaxation times outside of the MRI, 300 m isotropic resolution images were acquired, and image registration methods applied to measure 3D internal strain. In conclusion, new methods to visualize and quantify CEP thickness, annular tear detection and geometric quantification, and non-invasively measure 3D internal disc strains were established. No correlation was found between CEP thickness and disc level; however the periphery was significantly thicker compared to central locations. Clear distinction of adjacent AF lamellae enabled annular tear detection and detailed geometric quantification. Annular tears demonstrated non-classic geometry through interconnecting radial, circumferential, and perinuclear formations. Regional strain inhomogeneity was observed qualitatively and quantitatively. Variation in strain magnitudes might be explained by geometry in axial and circumferential strain while peak radial strain in the posterior AF may have important implications for disc herniation

Application of PS-InSAR Method for the Land Subsidence Analysis Using StaMPS (Case Study : Gresik Regency)

Land Subsudence often occurs in various regions around the world, especially big cities and coastal areas. The poor impact of land subsidence may the destruction of a region's infrastructure which caused by excessive water taking for industrial use and existing soil forming structures in the area. Therefore, it is necessary to find various inventions with the aim to mitigate natural disasters accurately. Along with the development of technology, then used adequate technology that has wide area capability. The selection of PS-InSAR method based on Radar becomes the best solution because it has good accuracy and decrease the decorrelation effect. The method used by PS-InSAR in the process of land subsidence in Gresik Regency using StaMPS at the same time with the decrease of ground level between -49.35 mm / year to 54,95 mm / year. Bungah Sub-district has the maximum value from the period before May 2015 to January 2016