MR-guided stereotactic navigation

Functional magnetic resonance imaging allows precise localization of brain regions specialized for different perceptual and higher cognitive functions. However, targeting these deep brain structures for electrophysiology still remains a challenging task. Here, we propose a novel framework for MRI-stereotactic registration and chamber placement for precise electrode guidance to recording sites defined in MRI space. The proposed “floating frame” approach can be used without usage of ear bars, greatly reducing pain and discomfort common in standard stereotactic surgeries. Custom pre-surgery planning software was developed to automatically solve the registration problem and report the set of parameters needed to position a stereotactic manipulator to reach a recording site along arbitrary, non-vertical trajectories. Furthermore, the software can automatically identify blood vessels and assist in finding safe trajectories to targets. Our approach was validated by targeting different regions in macaque monkeys and rats. We expect that our method will facilitate recording in new brain areas and provide a valuable tool for electrophysiologists

A pseudo active kinematic constraint for a biological living soft tissue: an effect of the collagen network

Recent studies in mammalian hearts show that left ventricular wall thickening is an important mechanism for systolic ejection and that during contraction the cardiac muscle develops significant stresses in the muscular cross-fiber direction. We suggested that the collagen network surrounding the muscular fibers could account for these mechanical behaviors. To test this hypothesis we develop a model for large deformation response of active, incompressible, nonlinear elastic and transversely isotropic living soft tissue (such as cardiac or arteries tissues) in which we include a coupling effect between the connective tissue and the muscular fibers. Then, a three-dimensional finite element formulation including this internal pseudo-active kinematic constraint is derived. Analytical and finite element solutions are in a very good agreement. The numerical results show this wall thickening effect with an order of magnitude compatible with the experimental observations

CONFIGEN: A tool for managing configuration options

This paper introduces CONFIGEN, a tool that helps modularizing software. CONFIGEN allows the developer to select a set of elementary components for his software through an interactive interface. Configuration files for use by C/assembly code and Makefiles are then automatically generated, and we successfully used it as a helper tool for complex system software refactoring. CONFIGEN is based on propositional logic, and its implementation faces hard theoretical problems.Comment: In Proceedings LoCoCo 2010, arXiv:1007.083

Mixed variational formulations of finite element analysis of elastoacoustic/slosh fluid-structure interaction

A general three-field variational principle is obtained for the motion of an acoustic fluid enclosed in a rigid or flexible container by the method of canonical decomposition applied to a modified form of the wave equation in the displacement potential. The general principle is specialized to a mixed two-field principle that contains the fluid displacement potential and pressure as independent fields. This principle contains a free parameter alpha. Semidiscrete finite-element equations of motion based on this principle are displayed and applied to the transient response and free-vibrations of the coupled fluid-structure problem. It is shown that a particular setting of alpha yields a rich set of formulations that can be customized to fit physical and computational requirements. The variational principle is then extended to handle slosh motions in a uniform gravity field, and used to derive semidiscrete equations of motion that account for such effects

Coupled fluid-structure interaction. Part 1: Theory. Part 2: Application

A general three dimensional variational principle is obtained for the motion of an acoustic field enclosed in a rigid or flexible container by the method of canonical decomposition applied to a modified form of the wave equation in the displacement potential. The general principle is specialized to a mixed two-field principle that contains the fluid displacement potential and pressure as independent fields. Semidiscrete finite element equations of motion based on this principle are derived and sample cases are given