Publications by Year: 2008


Tokuda J, Fischer GS, Csoma C, Dimaio SP, Gobbi DG, Fichtinger G, Tempany CM, Hata N. Software strategy for robotic transperineal prostate therapy in closed-bore MRI. Med Image Comput Comput Assist Interv. 2008;11(Pt 2):701–9.
A software strategy to provide intuitive navigation for MRI-guided robotic transperineal prostate therapy is presented. In the system, the robot control unit, the MRI scanner, and open-source navigation software are connected to one another via Ethernet to exchange commands, coordinates, and images. Six states of the system called "workphases" are defined based on the clinical scenario to synchronize behaviors of all components. The wizard-style user interface allows easy following of the clinical workflow. On top of this framework, the software provides features for intuitive needle guidance: interactive target planning; 3D image visualization with current needle position; treatment monitoring through real-time MRI. These features are supported by calibration of robot and image coordinates by the fiducial-based registration. The performance test shows that the registration error of the system was 2.6 mm in the prostate area, and it displayed real-time 2D image 1.7 s after the completion of image acquisition.
Maddah M, Zöllei L, Grimson EL, Westin CF, Wells WM. A Mathematical Framework for Incorporating Anatomical Knowledge in DT-MRI Analysis. Proc IEEE Int Symp Biomed Imaging. 2008;4543943:105–108.
We propose a Bayesian approach to incorporate anatomical information in the clustering of fiber trajectories. An expectation-maximization (EM) algorithm is used to cluster the trajectories, in which an atlas serves as the prior on the labels. The atlas guides the clustering algorithm and makes the resulting bundles anatomically meaningful. In addition, it provides the seed points for the tractography and initial settings of the EM algorithm. The proposed approach provides a robust and automated tool for tract-oriented analysis both in a single subject and over a population.
Yeo BTT, Sabuncu M, Vercauteren T, Ayache N, Fischl B, Golland P. Spherical demons: fast surface registration. Med Image Comput Comput Assist Interv. 2008;11(Pt 1):745–53.
We present the fast Spherical Demons algorithm for registering two spherical images. By exploiting spherical vector spline interpolation theory, we show that a large class of regularizers for the modified demons objective function can be efficiently implemented on the sphere using convolution. Based on the one parameter subgroups of diffeomorphisms, the resulting registration is diffeomorphic and fast - registration of two cortical mesh models with more than 100k nodes takes less than 5 minutes, comparable to the fastest surface registration algorithms. Moreover, the accuracy of our method compares favorably to the popular FreeSurfer registration algorithm. We validate the technique in two different settings: (1) parcellation in a set of in-vivo cortical surfaces and (2) Brodmann area localization in ex-vivo cortical surfaces.
Tricoche X, Kindlmann G, Westin CF. Invariant crease lines for topological and structural analysis of tensor fields. IEEE Trans Vis Comput Graph. 2008;14(6):1627–34.
We introduce a versatile framework for characterizing and extracting salient structures in three-dimensional symmetric second-order tensor fields. The key insight is that degenerate lines in tensor fields, as defined by the standard topological approach, are exactly crease (ridge and valley) lines of a particular tensor invariant called mode. This reformulation allows us to apply well-studied approaches from scientific visualization or computer vision to the extraction of topological lines in tensor fields. More generally, this main result suggests that other tensor invariants, such as anisotropy measures like fractional anisotropy (FA), can be used in the same framework in lieu of mode to identify important structural properties in tensor fields. Our implementation addresses the specific challenge posed by the non-linearity of the considered scalar measures and by the smoothness requirement of the crease manifold computation. We use a combination of smooth reconstruction kernels and adaptive refinement strategy that automatically adjust the resolution of the analysis to the spatial variation of the considered quantities. Together, these improvements allow for the robust application of existing ridge line extraction algorithms in the tensor context of our problem. Results are proposed for a diffusion tensor MRI dataset, and for a benchmark stress tensor field used in engineering research.
Malcolm J, Rathi Y, Shenton ME, Tannenbaum A. Label space: a coupled multi-shape representation. Med Image Comput Comput Assist Interv. 2008;11(Pt 2):416–24.
Richly labeled images representing several sub-structures of an organ occur quite frequently in medical images. For example, a typical brain image can be labeled into grey matter, white matter or cerebrospinal fluid, each of which may be subdivided further. Many manipulations such as interpolation, transformation, smoothing, or registration need to be performed on these images before they can be used in further analysis. In this work, we present a novel multi-shape representation and compare it with the existing representations to demonstrate certain advantages of using the proposed scheme. Specifically, we propose label space, a representation that is both flexible and well suited for coupled multi-shape analysis. Under this framework, object labels are mapped to vertices of a regular simplex, e.g. the unit interval for two labels, a triangle for three labels, a tetrahedron for four labels, etc. This forms the basis of a convex linear structure with the property that all labels are equally spaced. We will demonstrate that this representation has several desirable properties: algebraic operations may be performed directly, label uncertainty is expressed equivalently as a weighted mixture of labels or in a probabilistic manner, and interpolation is unbiased toward any label or the background. In order to demonstrate these properties, we compare label space to signed distance maps as well as other implicit representations in tasks such as smoothing, interpolation, registration, and principal component analysis.
Kubicki M, Styner MA, Bouix S, Gerig G, Markant D, Smith K, Kikinis R, McCarley RW, Shenton ME. Reduced Interhemispheric Connectivity in Schizophrenia- Tractography Based Segmentation of the Corpus Callosum. Schizophr Res. 2008;106(2-3):125–31.
BACKGROUND: A reduction in interhemispheric connectivity is thought to contribute to the etiology of schizophrenia. Diffusion Tensor Imaging (DTI) measures the diffusion of water and can be used to describe the integrity of the corpus callosum white matter tracts, thereby providing information concerning possible interhemispheric connectivity abnormalities. Previous DTI studies in schizophrenia are inconsistent in reporting decreased Fractional Anisotropy (FA), a measure of anisotropic diffusion, within different portions of the corpus callosum. Moreover, none of these studies has investigated corpus callosum systematically, using anatomical subdivisions. METHODS: DTI and structural MRI scans were obtained from 32 chronic schizophrenic subjects and 42 controls. Corpus callosum cross sectional area and its probabilistic subdivisions were determined automatically from structural MRI scans using a model based deformable contour segmentation. These subdivisions employ a previously generated probabilistic subdivision atlas, based on fiber tractography and anatomical lobe subdivision. The structural scan was then co-registered with the DTI scan and the anatomical corpus callosum subdivisions were propagated to the associated FA map. RESULTS: Results revealed decreased FA within parts of the corpus interconnecting frontal regions in schizophrenia compared with controls, but no significant changes for callosal fibers interconnecting parietal and temporo-occipital brain regions. In addition, integrity of the anterior corpus was statistically significantly correlated with negative as well as positive symptoms, while posterior measures correlated with positive symptoms only. CONCLUSIONS: This study provides quantitative evidence for a reduction of interhemispheric brain connectivity in schizophrenia, involving corpus callosum, and further points to frontal connections as possibly disrupted in schizophrenia.
Yeo BTT, Yu P, Grant E, Fischl B, Golland P. Shape analysis with overcomplete spherical wavelets. Med Image Comput Comput Assist Interv. 2008;11(Pt 1):468–76.
In this paper, we explore the use of over-complete spherical wavelets in shape analysis of closed 2D surfaces. Previous work has demonstrated, theoretically and practically, the advantages of overcomplete over bi-orthogonal spherical wavelets. Here we present a detailed formulation of over-complete wavelets, as well as shape analysis experiments of cortical folding development using them. Our experiments verify in a quantitative fashion existing qualitative theories of neuroanatomical development. Furthermore, the experiments reveal novel insights into neuro-anatomical development not previously documented.
Lankton S, Tannenbaum A. Localizing region-based active contours. IEEE Trans Image Process. 2008;17(11):2029–39.
In this paper, we propose a natural framework that allows any region-based segmentation energy to be re-formulated in a local way. We consider local rather than global image statistics and evolve a contour based on local information. Localized contours are capable of segmenting objects with heterogeneous feature profiles that would be difficult to capture correctly using a standard global method. The presented technique is versatile enough to be used with any global region-based active contour energy and instill in it the benefits of localization. We describe this framework and demonstrate the localization of three well-known energies in order to illustrate how our framework can be applied to any energy. We then compare each localized energy to its global counterpart to show the improvements that can be achieved. Next, an in-depth study of the behaviors of these energies in response to the degree of localization is given. Finally, we show results on challenging images to illustrate the robust and accurate segmentations that are possible with this new class of active contour models.
Van Leemput K, Bakkour A, Benner T, Wiggins G, Wald LL, Augustinack J, Dickerson BC, Golland P, Fischl B. Model-based segmentation of hippocampal subfields in ultra-high resolution in vivo MRI. Med Image Comput Comput Assist Interv. 2008;11(Pt 1):235–43.
Recent developments in MR data acquisition technology are starting to yield images that show anatomical features of the hippocampal formation at an unprecedented level of detail, providing the basis for hippocampal subfield measurement. Because of the role of the hippocampus in human memory and its implication in a variety of disorders and conditions, the ability to reliably and efficiently quantify its subfields through in vivo neuroimaging is of great interest to both basic neuroscience and clinical research. In this paper, we propose a fully-automated method for segmenting the hippocampal subfields in ultra-high resolution MRI data. Using a Bayesian approach, we build a computational model of how images around the hippocampal area are generated, and use this model to obtain automated segmentations. We validate the proposed technique by comparing our segmentation results with corresponding manual delineations in ultra-high resolution MRI scans of five individuals.
Ziyan U, Westin CF. Joint segmentation of thalamic nuclei from a population of diffusion tensor MR images. Med Image Comput Comput Assist Interv. 2008;11(Pt 1):279–86.
Several recent studies explored the use of unsupervised segmentation methods for segmenting thalamic nuclei from diffusion tensor images. These methods provide a plausible segmentation on individual subjects; however, they do not address the problem of consistently identifying the same functional areas in a population. The lack of correspondence between the segmented nuclei make it more difficult to use the results from the unsupervised segmentation tools for morphometry. In this paper we present a novel segmentation algorithm to automatically segment the gray matter nuclei while ensuring consistency between subjects in a population. This new algorithm, referred to as Consistency Clustering, finds correspondence between the nuclei as the segmentation is achieved through a single model for the whole population, similar to the brain atlases experts use to identify thalamic nuclei.