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Current Projects


Multiscale Shape Segmentation Techniques

To represent multiscale variations in a shape population in order to drive the segmentation of deep brain structures, such as the caudate nucleus or the hippocampus.

New: Delphine Nain won the best student paper at MICCAI 2006 in the category "Segmentation and Registration" for her paper entitled "Shape-driven surface segmentation using spherical wavelets" by D. Nain, S. Haker, A. Bobick, A. Tannenbaum.

Rule-Based Segmentation Techniques

In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules.

New: Al-Hakim, et al. Parcellation of the Striatum. SPIE MI 2007.

Kernel PCA for Segmentation

Segmentation performances using active contours can be drastically improved if the possible shapes of the object of interest are learnt. The goal of this work is to use Kernel PCA to learn shape priors. Kernel PCA allows for learning non linear dependencies in data sets, leading to more robust shape priors.

New: S. Dambreville, Y. Rathi, and A. Tannenbaum. A Framework for Image Segmentation using Image Shape Models and Kernel PCA Shape Priors. PAMI. Submitted to PAMI.

Blood Vessel Segmentation

The goal of this work is to develop blood vessel segmentation techniques for 3D MRI and CT data. The methods have been applied to coronary arteries and portal veins, with promising results.

New: Y. Yang, S. George, D. Martin, A. Tannenbaum, and D. Giddens. 3D Modeling of Patient-Specific Geometries of Portal Veins Using MR Images. In Proceedings IEEE EMBS, 2006

Knowledge-Based Bayesian Segmentation

This ITK filter is a segmentation algorithm that utilizes Bayes's Rule along with an affine-invariant anisotropic smoothing filter.

New: J. Melonakos, K. Krishnan, and A. Tannenbaum. An ITK Filter for Bayesian Segmentation: itkBayesianClassifierImageFilter. Insight Journal, 2006.

Stochastic Methods for Segmentation

New stochastic methods for implementing curvature driven flows for various medical tasks such as segmentation.

New: Currently under investigation.


Conformal Flattening

The goal of this project is for better visualizing and computation of neural activity from fMRI brain imagery. Also, with this technique, shapes can be mapped to shperes for shape analysis, registration or other purposes. Our technique is based on conformal mappings which map genus-zero surface: in fmri case cortical or other surfaces, onto a sphere in an angle preserving manner.

New: Y. Gao, J. Melonakos, and A. Tannenbaum. Conformal Flattening ITK Filter. ISC/NA-MIC Workshop on Open Science at MICCAI 2006.

Optimal Mass Transport Registration

The goal of this project is to implement a computationaly efficient Elastic/Non-rigid Registration algorithm based on the Monge-Kantorovich theory of optimal mass transport for 3D Medical Imagery. Our technique is based on Multigrid and Multiresolution techniques. This method is particularly useful because it is parameter free and utilizes all of the grayscale data in the image pairs in a symmetric fashion and no landmarks need to be specified for correspondence.

New: Tauseef ur Rehman, A. Tannenbaum. Multigrid Optimal Mass Transport for Image Registration and Morphing. Accepted for SPIE Conference on Computational Imaging, Jan 2007.

DWI Processing

Finsler Active Contour DWI Tractography

In this work, we provide an energy minimization framework which allows one to find optimal curves in direction-dependent data (i.e. where the cost associated with the curve depends both upon its position and orientation)

New: E. Pichon, J. Melonakos, S. Angenet, A. Tannenbaum. Publication currently under review.

Shape Analysis

Multiscale Shape Analysis

We present a novel method of statistical surface-based morphometry based on the use of non-parametric permutation tests and a spherical wavelet (SWC) shape representation.

New: D. Nain, M. Styner, M. Niethammer, J. J. Levitt, M E Shenton, G Gerig, A. Bobick, A. Tannenbaum. Statistical Shape Analysis of Brain Structures using Spherical Wavelets. Submitted to ISBI 2007.

Centerline Generation for Vessels

The goal of this work is to generate centerlines from segmented 3D surfaces of blood vessels using a harmonic skeletonization technique. The generated centerlines are used as a guide to visualize and evaluate stenoses in human coronary arteries.

KPCA, LLE, KLLE Shape Analysis

The goal of this work is to study and compare shape learning techniques. The techniques considered are Linear Principal Components Analysis (PCA), Kernel PCA, Locally Linear Embedding (LLE) and Kernel LLE.

Completed Projects


Fast Marching Slicer 2 Module

The Fast Marching Algorithm was added as a module to Slicer 2.

Statistical/PDE Methods for Segmentation

This flow was added to Slicer 2.

Image Smooth Slicer 2 Module

2D and 3D smoothing of images.

Affine Segment Slicer 2 Module

This module can be used to perform edge based segmentation.