Inferring Geodesic Cerebrovascular Graphs: Image Processing, Topological Alignment and Biomarkers Extraction

A vectorial representation of the vascular network that embodies quantitative features - location, direction, scale, and bifurcations - has many potential neuro-vascular applications. Patient-specific models support computer-assisted surgical procedures in neurovascular interventions, while analyses on multiple subjects are essential for group-level studies on which clinical prediction and therapeutic inference ultimately depend. This first motivated the development of a variety of methods to segment the cerebrovascular system. Nonetheless, a number of limitations, ranging from data-driven inhomogeneities, the anatomical intra- and inter-subject variability, the lack of exhaustive ground-truth, the need for operator-dependent processing pipelines, and the highly non-linear vascular domain, still make the automatic inference of the cerebrovascular topology an open problem. In this thesis, brain vessels’ topology is inferred by focusing on their connectedness. With a novel framework, the brain vasculature is recovered from 3D angiographies by solving a connectivity-optimised anisotropic level-set over a voxel-wise tensor field representing the orientation of the underlying vasculature. Assuming vessels joining by minimal paths, a connectivity paradigm is formulated to automatically determine the vascular topology as an over-connected geodesic graph. Ultimately, deep-brain vascular structures are extracted with geodesic minimum spanning trees. The inferred topologies are then aligned with similar ones for labelling and propagating information over a non-linear vectorial domain, where the branching pattern of a set of vessels transcends a subject-specific quantized grid. Using a multi-source embedding of a vascular graph, the pairwise registration of topologies is performed with the state-of-the-art graph matching techniques employed in computer vision. Functional biomarkers are determined over the neurovascular graphs with two complementary approaches. Efficient approximations of blood flow and pressure drop account for autoregulation and compensation mechanisms in the whole network in presence of perturbations, using lumped-parameters analog-equivalents from clinical angiographies. Also, a localised NURBS-based parametrisation of bifurcations is introduced to model fluid-solid interactions by means of hemodynamic simulations using an isogeometric analysis framework, where both geometry and solution profile at the interface share the same homogeneous domain. Experimental results on synthetic and clinical angiographies validated the proposed formulations. Perspectives and future works are discussed for the group-wise alignment of cerebrovascular topologies over a population, towards defining cerebrovascular atlases, and for further topological optimisation strategies and risk prediction models for therapeutic inference. Most of the algorithms presented in this work are available as part of the open-source package VTrails

Navier-Stokes Modelling of Non-Newtonian Blood Flow in Cerebral Arterial Circulation and its Dynamic Impact on Electrical Conductivity in a Realistic Multi-Compartment Head Model

Background and Objective: This study aims to evaluate the dynamic effect of non-Newtonian cerebral arterial circulation on electrical conductivity distribution (ECD) in a realistic multi-compartment head model. It addresses the importance and challenges associated with electrophysiological modalities, such as transcranial electrical stimulation, electro-magnetoencephalography, and electrical impedance tomography. Factors such as electrical conductivity's impact on forward modeling accuracy, complex vessel networks, data acquisition limitations (especially in MRI), and blood flow phenomena are considered. Methods: The Navier-Stokes equations (NSEs) govern the non-Newtonian flow model used in this study. The solver comprises two stages: the first solves the pressure field using a dynamical pressure-Poisson equation derived from NSEs, and the second updates the velocity field using Leray regularization and the pressure distribution from the first stage. The Carreau-Yasuda model establishes the connection between blood velocity and viscosity. Blood concentration in microvessels is approximated using Fick's law of diffusion, and conductivity mapping is obtained via Archie's law. The head model used corresponds to an open 7 Tesla MRI dataset, differentiating arterial vessels from other structures. Results: The results suggest the establishment of a dynamic model of cerebral blood flow for arterial and microcirculation. Blood pressure and conductivity distributions are obtained through numerically simulated pulse sequences, enabling approximation of blood concentration and conductivity within the brain. Conclusions: This model provides an approximation of dynamic blood flow and corresponding ECD in different brain regions. The advantage lies in its applicability with limited a priori information about blood flow and compatibility with arbitrary head models that distinguish arteries.Comment: 13 pages; 8 figures; 2 tabl

Simple Patient-Based Transmantle Pressure and Shear Estimate From Cine Phase-Contrast MRI in Cerebral Aqueduct

From measurements of the oscillating flux of the cerebrospinal fluid (CSF) in the aqueduct of Sylvius, we elaborate a patient-based methodology for transmantle pressure (TRP) and shear evaluation. High-resolution anatomical magnetic resonance imaging first permits a precise 3-D anatomical digitalized reconstruction of the Sylvius’s aqueduct shape. From this, a very fast approximate numerical flow computation, nevertheless consistent with analytical predictions, is developed. Our approach includes the main contributions of inertial effects coming from the pulsatile flow and curvature effects associated with the aqueduct bending. Integrating the pressure along the aqueduct longitudinal center-line enables the total dynamic hydraulic admittances of the aqueduct to be evaluated, which is the pre-eminent contribution to the CSF pressure difference between the lateral ventricles and the subarachnoidal spaces also called the TRP. The application of the method to 20 healthy human patients validates the hypothesis of the proposed approach and provides a first database for normal aqueduct CSF flow. Finally, the implications of our results for modeling and evaluating intracranial cerebral pressure are discussed

Automatic 2-D/3-D Vessel Enhancement in Multiple Modality Images Using a Weighted Symmetry Filter

Automated detection of vascular structures is of great importance in understanding the mechanism, diagnosis and treatment of many vascular pathologies. However, automatic vascular detection continues to be an open issue because of difficulties posed by multiple factors such as poor contrast, inhomogeneous backgrounds, anatomical variations, and the presence of noise during image acquisition. In this paper, we propose a novel 2D/3D symmetry filter to tackle these challenging issues for enhancing vessels from different imaging modalities. The proposed filter not only considers local phase features by using a quadrature filter to distinguish between lines and edges, but also uses the weighted geometric mean of the blurred and shifted responses of the quadrature filter, which allows more tolerance of vessels with irregular appearance. As a result, this filter shows a strong response to the vascular features under typical imaging conditions. Results based on 8 publicly available datasets (six 2D datasets, one 3D dataset and one 3D synthetic dataset) demonstrate its superior performance to other state-ofthe- art methods

Finsler Active Contours

©2008 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or distribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder.DOI: 10.1109/TPAMI.2007.70713In this paper, we propose an image segmentation technique based on augmenting the conformal (or geodesic) active contour framework with directional information. In the isotropic case, the euclidean metric is locally multiplied by a scalar conformal factor based on image information such that the weighted length of curves lying on points of interest (typically edges) is small. The conformal factor that is chosen depends only upon position and is in this sense isotropic. Although directional information has been studied previously for other segmentation frameworks, here, we show that if one desires to add directionality in the conformal active contour framework, then one gets a well-defined minimization problem in the case that the factor defines a Finsler metric. Optimal curves may be obtained using the calculus of variations or dynamic programming-based schemes. Finally, we demonstrate the technique by extracting roads from aerial imagery, blood vessels from medical angiograms, and neural tracts from diffusion-weighted magnetic resonance imagery

Coronary Artery Segmentation and Motion Modelling

Conventional coronary artery bypass surgery requires invasive sternotomy and the use of a cardiopulmonary bypass, which leads to long recovery period and has high infectious potential. Totally endoscopic coronary artery bypass (TECAB) surgery based on image guided robotic surgical approaches have been developed to allow the clinicians to conduct the bypass surgery off-pump with only three pin holes incisions in the chest cavity, through which two robotic arms and one stereo endoscopic camera are inserted. However, the restricted field of view of the stereo endoscopic images leads to possible vessel misidentification and coronary artery mis-localization. This results in 20-30% conversion rates from TECAB surgery to the conventional approach. We have constructed patient-specific 3D + time coronary artery and left ventricle motion models from preoperative 4D Computed Tomography Angiography (CTA) scans. Through temporally and spatially aligning this model with the intraoperative endoscopic views of the patient's beating heart, this work assists the surgeon to identify and locate the correct coronaries during the TECAB precedures. Thus this work has the prospect of reducing the conversion rate from TECAB to conventional coronary bypass procedures. This thesis mainly focus on designing segmentation and motion tracking methods of the coronary arteries in order to build pre-operative patient-specific motion models. Various vessel centreline extraction and lumen segmentation algorithms are presented, including intensity based approaches, geometric model matching method and morphology-based method. A probabilistic atlas of the coronary arteries is formed from a group of subjects to facilitate the vascular segmentation and registration procedures. Non-rigid registration framework based on a free-form deformation model and multi-level multi-channel large deformation diffeomorphic metric mapping are proposed to track the coronary motion. The methods are applied to 4D CTA images acquired from various groups of patients and quantitatively evaluated