Isosurface extraction from brain images often creates handles between brain folds that are anatomically separated. Although manual editing could optimally correct these anatomical errors, it is not realistic due the size of the 3D data and the convoluted geometry of the brain. We propose an algorithm to automatically repair the isosurface and we make our code available at http://www.OpenTopology.org

Open Topology: A Toolkit for Brain Isosurface Correction

OpenTissue is a multidisciplinary, open source programming toolkit
 for physics-based simulation, collision detection, scientific
 visualization, and medical imaging. The toolkit was initiated in
 2001, is driven by academia, and is used by several universities.
 It implements several cutting edge simulators using cutting edge
 programming techniques. OpenTissue is available under Windows and
 Linux, and it implements almost all algorithms presented in the
 accompanying book, Erleben et al. Physics-Based Animation, Charles River Media, 2005. This
 presentation will give an overview of OpenTissue: what it can do,
 how it is done, and where the toolkit is going

OpenTissue - An Open Source Toolkit for Physics-Based Animation

Since the 1970's B-splines have evolved to become the {\em de facto} 
standard for curve and surface representation due to many
of their salient properties. Conventional least-squares 
scattered data fitting techniques for B-splines require the inversion 
of potentially large matrices. This is time-consuming as well 
as susceptible to ill-conditioning which leads to undesired
results. Lee {\em et al.} proposed a novel B-spline 
algorithm for fitting a 2-D cubic B-spline surface to scattered 
data in \cite{Lee}. The proposed algorithm utilizes an 
optional multilevel approach for better fitting results. 
We generalize this technique to support N-dimensional 
data fitting as well as arbitrary degree of B-spline. In addition, 
we generalize the B-spline kernel function class to accommodate 
this new image filter.

N-D $C^k$ B-Spline Scattered Data Approximation

Binary morphological closing and opening image filters remove structures smaller than the structuring element in a binary image.

Binary morphological closing and opening image filters

InvertIntensityImageFilter is a convenient filter to invert the intensity of an image.

InvertIntensityImageFilter

Morphological gradients enhance the variation of pixel intensity in a given neighborhood.

MorphologicalGradientImageFilter

ModulusImageFilter is a simple image filter to compute the modulus (x % dividend) pixel-wise.

ModulusImageFilter

A report on the issue of image orientation with respect to the Insight Toolkit. A description of how orientation is defined in ITK, and the tools available for manipulating and detecting image orientation.

A definition of Spatial Orientation for the Insight Toolkit

A filter to impose to the input image the minima defined in the marker image.