NA-MIC Internal Collaborations:StructuralImageAnalysis

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Structural Image Analysis

Image Segmentation

	Brachytherapy Needle Positioning Robot Integration The Queen’s/Hopkins team is developing novel devices and procedures for cancer interventions, including biopsy and therapies. Our goal for the programming week is to design and start implementing software for the new MRI Brachytherapy needle positioning robot. More... New: Meeting at JHU on July 17-19, 2007.
	Knowledge-Based Bayesian Segmentation This ITK filter is a segmentation algorithm that utilizes Bayes's Rule along with an affine-invariant anisotropic smoothing filter. More... New: J. Melonakos, Y. Gao, and A. Tannenbaum. Tissue Tracking: Applications for Brain MRI Classification. SPIE Medical Imaging, 2007.
	Tubular Surface Segmentation Framework We have proposed a new model for tubular surfaces that transforms the problem of detecting a surface in 3D space, to detecting a curve in 4D space. Besides allowing us to impose a "soft" tubular shape prior, this also leads to computational efficiency over conventional surface segmentation approaches. More...
	Rule-Based Striatum Segmentation In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules for the striatum. More... New: Al-Hakim, et al. Parcellation of the Striatum. SPIE MI 2007.
	Rule-Based DLPFC Segmentation In this work, we provide software to semi-automate the implementation of segmentation procedures based on expert neuroanatomist rules for the dorsolateral prefrontal cortex. More... New: Al-Hakim R, Nain D, Melonakos J, Tannenbaum A, Fallon J. A Dorsolateral Prefrontal Cortex Semi-Automatic Segmenter. Proc SPIE Medical Imaging, 2006.
	Re-Orientation Approach for Segmentation of DW-MRI This work proposes a methodology to segment tubular fiber bundles from diffusion weighted magnetic resonance images (DW-MRI). Segmentation is simplified by locally reorienting diffusion information based on large-scale fiber bundle geometry. More...
	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. More... 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.
	Stochastic Methods for Segmentation New stochastic methods for implementing curvature driven flows for various medical tasks such as segmentation. More... New: Currently under investigation.
	Statistical/PDE Methods using Fast Marching for Segmentation This Fast Marching based flow was added to Slicer 2. More...
	Tissue Classification with Neighborhood Statistics We have implemented an MRI tissue classification algorithm based on unsupervised non-parametric density estimation of tissue intensity classes. More... T Tasdizen, S Awate, R Whitaker, A nonparametric, entropy-minimizing MRI tissue classification algorithm implementation using ITK, MICCAI 2005 Open-Source Workshop.
	Atlas Renormalization for Improved Brain MR Image Segmentation across Scanner Platforms Atlas-based approaches have demonstrated the ability to automatically identify detailed brain structures from 3-D magnetic resonance (MR) brain images. Unfortunately, the accuracy of this type of method often degrades when processing data acquired on a different scanner platform or pulse sequence than the data used for the atlas training. In this paper, we improve the performance of an atlas-based whole brain segmentation method by introducing an intensity renormalization procedure that automatically adjusts the prior atlas intensity model to new input data. Validation using manually labeled test datasets has shown that the new procedure improves the segmentation accuracy (as measured by the Dice coefficient) by 10% or more for several structures including hippocampus, amygdala, caudate, and pallidum. The results verify that this new procedure reduces the sensitivity of the whole brain segmentation method to changes in scanner platforms and improves its accuracy and robustness, which can thus facilitate multicenter or multisite neuroanatomical imaging studies. More... New: IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007

Image Registration

	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. More... New: Tauseef ur Rehman, A. Tannenbaum. Multigrid Optimal Mass Transport for Image Registration and Morphing. SPIE Conference on Computational Imaging V, Jan 2007.
	Diffusion Tensor Image Processing Tools We implement the diffusion weighted image (DWI) registration model from the paper of G.K.Rohde et al. Patient head motion and eddy currents distortion cause artifacts in maps of diffusion parameters computer from DWI. This model corrects these two distortions at the same time including brightness correction. New: We have recently developed software for eddy current correction.
	Non-Rigid EPI Registration Our Objective is to identify optimal ITK method and parameter settings for non-rigid intrasubject registration of T2 EPI, the raw building block images of DTI, to T1 conventional images. Provide software devliverable. More... New: Project Week Results: Jan 2006
	Cortical Correspondence using Particle System In this project, we want to compute cortical correspondence on populations, using various features such as cortical structure, DTI connectivity, vascular structure, and functional data (fMRI). This presents a challenge because of the highly convoluted surface of the cortex, as well as because of the different properties of the data features we want to incorporate together. More... New: IPMI 2009 paper Incorporating DTI data in cortical correspondence completed.
	Population Analysis from Deformable Registration Analysis of populations of diffusion images typically requires time-consuming manual segmentation of structures of interest to obtain correspondance for statistics. This project uses non-rigid registration of DTI images to produce a common coordinate system for hypothesis testing of diffusion properties. More... New: Command line DTI tools available as part of UNC NeuroLib
	Point Set Rigid Registration In this work, we propose a particle filtering approach for the problem of registering two point sets that differ by a rigid body transformation. Experimental results are provided that demonstrate the robustness of the algorithm to initialization, noise, missing structures or differing point densities in each sets, on challenging 2D and 3D registration tasks. More... New: R. Sandhu, S. Dambreville, A. Tannenbaum. Particle Filtering for Registration of 2D and 3D Point Sets with Stochastic Dynamics. In CVPR, 2008.
	Optimal Atlas Regularization in Image Segmentation We propose a unified framework for computing atlases from manually labeled data sets at various degrees of “sharpness” and the joint registration and segmentation of a new brain with these atlases. Using this framework, we investigate the tradeoff between warp regularization and image fidelity, i.e. the smoothness of the new subject warp and the sharpness of the atlas in a segmentation application. More... New: B.T.T. Yeo, M.R. Sabuncu, R. Desikan, B. Fischl, P. Golland. Effects of Registration Regularization and Atlas Sharpness on Segmentation Accuracy. In Proceedings of MICCAI: International Conference on Medical Image Computing and Computer Assisted Intervention, 683-691, 2007. MICCAI Young Scientist Award.
	Multimodal Atlas In this work, we propose and investigate an algorithm that jointly co-registers a collection of images while computing multiple templates. The algorithm, called iCluster, is used to compute multiple atlases for a given population. More... New: M.R. Sabuncu, M.E. Shenton, P. Golland. Joint Registration and Clustering of Images. In Proceedings of MICCAI 2007 Statistical Registration Workshop: Pair-wise and Group-wise Alignment and Atlas Formation, 47-54, 2007.
	Groupwise Registration We extend a previously demonstrated entropy based groupwise registration method to include a free-form deformation model based on B-splines. We provide an efficient implementation using stochastic gradient descents in a multi-resolution setting. We demonstrate the method in application to a set of 50 MRI brain scans and compare the results to a pairwise approach using segmentation labels to evaluate the quality of alignment. More... New: S.K. Balci, P. Golland, M.E. Shenton, W.M. Wells III. Free-Form B-spline Deformation Model for Groupwise Registration. In Proceedings of MICCAI 2007 Statistical Registration Workshop: Pair-wise and Group-wise Alignment and Atlas Formation, 23-30, 2007.

Morphometric Measures and 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. More... 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. Accepted in The Fourth IEEE International Symposium on Biomedical Imaging (ISBI ’07) that will be held April 12-15, 2007 in Metro Washington DC, USA.
	Population Analysis of Anatomical Variability Our goal is to develop mathematical approaches to modeling anatomical variability within and across populations using tools like local shape descriptors of specific regions of interest and global constellation descriptors of multiple ROI's. More... New: Mert R Sabuncu and Polina Golland. Structural Constellations for Population Analysis of Anatomical Variability.
	Shape Analysis With Overcomplete Wavelets In this work, we extend the Euclidean wavelets to the sphere. The resulting over-complete spherical wavelets are invariant to the rotation of the spherical image parameterization. We apply the over-complete spherical wavelet to cortical folding development More... New: B.T.T. Yeo, W. Ou, P. Golland. On the Construction of Invertible Filter Banks on the 2-Sphere. Yeo, Ou and Golland. Accepted to the IEEE Transactions on Image Processing. P. Yu, B.T.T. Yeo, P.E. Grant, B. Fischl, P. Golland. Cortical Folding Development Study based on Over-Complete Spherical Wavelets. In Proceedings of MMBIA: IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis, 2007.
	Shape Based Level Segmentation This class of algorithms explicitly manipulates the representation of the object boundary to fit the strong gradients in the image, indicative of the object outline. Bias in the boundary evolution towards the likely shapes improves the robustness of the segmentation results when the intensity information alone is insufficient for boundary detection. More...
	Shape Based Segmentation and Registration This type of algorithm assigns a tissue type to each voxel in the volume. Incorporating prior shape information biases the label assignment towards contiguous regions that are consistent with the shape model. More... New: K.M. Pohl, J. Fisher, S. Bouix, M. Shenton, R. W. McCarley, W.E.L. Grimson, R. Kikinis, and W.M. Wells. Using the Logarithm of Odds to Define a Vector Space on Probabilistic Atlases. Medical Image Analysis,11(6), pp. 465-477, 2007. Best Paper Award MICCAI 2006
	Adaptive, Particle-Based Sampling for Shapes and Complexes This research is a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wider range of problems than existing methods, including nonmanifold surfaces and objects of arbitrary topology. More... New: J Cates, PT Fletcher, M Styner, M Shenton, R Whitaker, Shape modeling and analysis with entropy-based particle systems, IPMI 2007, pp. 333-345.
	Shape Analysis Framework using SPHARM-PDM The UNC shape analysis is based on an analysis framework of objects with spherical topology, described mainly by sampled spherical harmonics SPHARM-PDM. The input of the shape analysis framework is a set of binary segmentations of a single brain structure, such as the hippocampus or caudate. These segmentations are converted into a shape description (SPHARM) with correspondence and analyzed via Hotelling T^2 two sample metric. More... New: First version of Shape Analysis Toolset available as part of UNC Neurolib open source (download) , this is to be added to the NAMIC toolkit. Slicer 3 module for whole shape analysis pipeline in progress (based on BatchMake and distributed computing using Condor)
	Shape Analysis of the Hippocampus Our objective is to examine hippocampal shape in patients with schizophrenia and healthy controls. More... New: Styner M, Lieberman JA, McClure RK, Weinberger DR, Jones DW, Gerig G.: Morphometric analysis of lateral ventricles in schizophrenia and healthy controls regarding genetic and disease-specific factors, Proc Natl Acad Sci USA. 2005 Mar 29;102(13):4872-7. Epub 2005 Mar 16.
	Population Based Correspondence We are developing methodology to automatically find dense point correspondences between a collection of polygonal genus 0 meshes. The advantage of this method is independence from indivisual templates, as well as enhanced modeling properties. The method is based on minimizing a cost function that describes the goodness of correspondence. Apart from a cost function derived from the description length of the model, we also employ a cost function working with arbitrary local features. We extended the original methods to use surface curvature measurements, which are independent to differences of object aligment. More... New: Software available as part of UNC Neurolib open source (website) Evaluation on lateral ventricles, hippocampi, caudates, striatum, femural bone. Outperforms standard MDL on complex structures.
	Spherical Wavelets Cortical Surface Shape Analysis Based on Spherical Wavelets. We introduce the use of over-complete spherical wavelets for shape analysis of 2D closed surfaces. Bi-orthogonal spherical wavelets have been proved to be powerful tools in the segmentation and shape analysis of 2D closed surfaces, but unfortunately they suffer from aliasing problems and are therefore not invariant to rotation of the underlying surface parameterization. In this paper, we demonstrate the theoretical advantage of over-complete wavelets over bi-orthogonal wavelets and illustrate their utility on both synthetic and real data. In particular, we show that the over-complete spherical wavelet transform enjoys significant advantages for the analysis of cortical folding development in a newborn dataset. More... New: IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007
	Topology Correction Geometrically-Accurate Topology-Correction of Cortical Surfaces using Non-Separating Loops. We propose a technique to accurately correct the spherical topology of cortical surfaces. Specifically,we construct a mapping from the original surface onto the sphere to detect topological defects as minimal nonhomeomorphic regions. The topology of each defect is then corrected by opening and sealing the surface along a set of nonseparating loops that are selected in a Bayesian framework. The proposed method is a wholly self-contained topology correction algorithm, which determines geometrically accurate, topologically correct solutions based on the magnetic resonance imaging (MRI) intensity profile and the expected local curvature. Applied to real data, our method provides topological corrections similar to those made by a trained operator. More... New: IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 26, NO. 4, APRIL 2007
	Local Statistical Analysis via Permutation Tests We have further developed a set of statistical testing methods that allow the analysis of local shape differences using the Hotelling T 2 two sample metric. Permutatioin tests are employed for the computation of statistical p-values, both raw and corrected for multiple comparisons. Resulting significance maps are easily visualized. Additional visualization of the group tests are provided via mean difference magnitude and vector maps, as well as maps of the group covariance information. Ongoing research focuses on incorporating covariates such as clinical scores into the testing scheme. More... New: Available as part of Shape Analysis Toolset in UNC Neurolib open source (download).
	Automatic Outlining of sulci on the brain surface We present a method to automatically extract certain key features on a surface. We apply this technique to outline sulci on the cortical surface of a brain. More...
	QDEC: An easy to use GUI for group morphometry studies Qdec is a application included in the Freesurfer software package intended to aid researchers in performing inter-subject / group averaging and inference on the morphometry data (cortical surface and volume) produced by the Freesurfer processing stream. The functionality in Qdec is also available as a processing module within Slicer3, and XNAT. More... See: Qdec user page