Publications

2011
Lee J, Lankton S, Tannenbaum A. Object tracking and target reacquisition based on 3-D range data for moving vehicles. IEEE Trans Image Process. 2011;20 (10) :2912-24.Abstract
In this paper, we propose an approach for tracking an object of interest based on 3-D range data. We employ particle filtering and active contours to simultaneously estimate the global motion of the object and its local deformations. The proposed algorithm takes advantage of range information to deal with the challenging (but common) situation in which the tracked object disappears from the image domain entirely and reappears later. To cope with this problem, a method based on principle component analysis (PCA) of shape information is proposed. In the proposed method, if the target disappears out of frame, shape similarity energy is used to detect target candidates that match a template shape learned online from previously observed frames. Thus, we require no a priori knowledge of the target's shape. Experimental results show the practical applicability and robustness of the proposed algorithm in realistic tracking scenarios.
Menze BH, Van Leemput K, Honkela A, Konukoglu E, Weber M-A, Ayache N, Golland P. A generative approach for image-based modeling of tumor growth. Inf Process Med Imaging. 2011;22 :735-47.Abstract
Extensive imaging is routinely used in brain tumor patients to monitor the state of the disease and to evaluate therapeutic options. A large number of multi-modal and multi-temporal image volumes is acquired in standard clinical cases, requiring new approaches for comprehensive integration of information from different image sources and different time points. In this work we propose a joint generative model of tumor growth and of image observation that naturally handles multimodal and longitudinal data. We use the model for analyzing imaging data in patients with glioma. The tumor growth model is based on a reaction-diffusion framework. Model personalization relies only on a forward model for the growth process and on image likelihood. We take advantage of an adaptive sparse grid approximation for efficient inference via Markov Chain Monte Carlo sampling. The approach can be used for integrating information from different multi-modal imaging protocols and can easily be adapted to other tumor growth models.
Glasser MF, Van Essen DC. Mapping human cortical areas in vivo based on myelin content as revealed by T1- and T2-weighted MRI. J Neurosci. 2011;31 (32) :11597-616.Abstract
Noninvasively mapping the layout of cortical areas in humans is a continuing challenge for neuroscience. We present a new method of mapping cortical areas based on myelin content as revealed by T1-weighted (T1w) and T2-weighted (T2w) MRI. The method is generalizable across different 3T scanners and pulse sequences. We use the ratio of T1w/T2w image intensities to eliminate the MR-related image intensity bias and enhance the contrast to noise ratio for myelin. Data from each subject were mapped to the cortical surface and aligned across individuals using surface-based registration. The spatial gradient of the group average myelin map provides an observer-independent measure of sharp transitions in myelin content across the surface--i.e., putative cortical areal borders. We found excellent agreement between the gradients of the myelin maps and the gradients of published probabilistic cytoarchitectonically defined cortical areas that were registered to the same surface-based atlas. For other cortical regions, we used published anatomical and functional information to make putative identifications of dozens of cortical areas or candidate areas. In general, primary and early unimodal association cortices are heavily myelinated and higher, multimodal, association cortices are more lightly myelinated, but there are notable exceptions in the literature that are confirmed by our results. The overall pattern in the myelin maps also has important correlations with the developmental onset of subcortical white matter myelination, evolutionary cortical areal expansion in humans compared with macaques, postnatal cortical expansion in humans, and maps of neuronal density in non-human primates.
Risholm P, Ross J, Washko GR, Wells III WM. Probabilistic Elastography: Estimating Lung Elasticity. Inf Process Med Imaging. 2011;22 :699-710.Abstract

We formulate registration-based elastography in a probabilistic framework and apply it to study lung elasticity in the presence of emphysematous and fibrotic tissue. The elasticity calculations are based on a Finite Element discretization of a linear elastic biomechanical model. We marginalize over the boundary conditions (deformation) of the biomechanical model to determine the posterior distribution over elasticity parameters. Image similarity is included in the likelihood, an elastic prior is included to constrain the boundary conditions, while a Markov model is used to spatially smooth the inhomogeneous elasticity. We use a Markov Chain Monte Carlo (MCMC) technique to characterize the posterior distribution over elasticity from which we extract the most probable elasticity as well as the uncertainty of this estimate. Even though registration-based lung elastography with inhomogeneous elasticity is challenging due the problem's highly underdetermined nature and the sparse image information available in lung CT, we show promising preliminary results on estimating lung elasticity contrast in the presence of emphysematous and fibrotic tissue.

Wassermann D, Rathi Y, Bouix S, Kubicki M, Kikinis R, Shenton M, Westin C-F. White Matter Bundle Registration and Population Analysis Based on Gaussian Processes. Inf Process Med Imaging. 2011;22 :320-32.Abstract

This paper proposes a method for the registration of white matter tract bundles traced from diffusion images and its extension to atlas generation, Our framework is based on a Gaussian process representation of tract density maps. Such a representation avoids the need for point-to-point correspondences, is robust to tract interruptions and reconnections and seamlessly handles the comparison and combination of white matter tract bundles. Moreover, being a parametric model, this approach has the potential to be defined in the Gaussian processes' parameter space, without the need for resampling the fiber bundles during the registration process. We use the similarity measure of our Gaussian process framework, which is in fact an inner product, to drive a diffeomorphic registration algorithm between two sets of homologous bundles which is not biased by point-to-point correspondences or the parametrization of the tracts. We estimate a dense deformation of the underlying white matter using the bundles as anatomical landmarks and obtain a population atlas of those fiber bundles. Finally we test our results in several different bundles obtained from in-vivo data.

Risholm P, Balter J, Wells III WM. Estimation of delivered dose in radiotherapy: the influence of registration uncertainty. Med Image Comput Comput Assist Interv. 2011;14 (Pt 1) :548-55.Abstract

We present a probabilistic framework to estimate the accumulated radiation dose and the corresponding dose uncertainty that is delivered to important anatomical structures, e.g. the primary tumor and healthy surrounding organs, during radiotherapy. The dose uncertainty we report is a direct result of uncertainties in the estimates of the deformation which aligns the daily cone-beam CT images with the planning CT. The accumulated radiation dose is an important measure to monitor during treatment, in particular to see if it significantly deviates from the planned dose which might indicate that either the patient was not properly positioned before treatment or that the anatomy has changed due to the treatment. In the case of the latter, the treatment plan should be adaptively changed to align with the current patient anatomy. We estimate the accumulated dose distribution, and its uncertainty, retrospectively on a dataset acquired during treatment of cancer in the neck and show the dose distributions in the form of dose volume histograms.

Gooya A, Pohl KM, Bilello M, Biros G, Davatzikos C. Joint segmentation and deformable registration of brain scans guided by a tumor growth model. Med Image Comput Comput Assist Interv. 2011;14 (Pt 2) :532-40.Abstract
This paper presents an approach for joint segmentation and deformable registration of brain scans of glioma patients to a normal atlas. The proposed method is based on the Expectation Maximization (EM) algorithm that incorporates a glioma growth model for atlas seeding, a process which modifies the normal atlas into one with a tumor and edema. The modified atlas is registered into the patient space and utilized for the posterior probability estimation of various tissue labels. EM iteratively refines the estimates of the registration parameters, the posterior probabilities of tissue labels and the tumor growth model parameters. We have applied this approach to 10 glioma scans acquired with four Magnetic Resonance (MR) modalities (T1, T1-CE, T2 and FLAIR) and validated the result by comparing them to manual segmentations by clinical experts. The resulting segmentations look promising and quantitatively match well with the expert provided ground truth.
Gaonkar B, Pohl K, Davatzikos C. Pattern based morphometry. Med Image Comput Comput Assist Interv. 2011;14 (Pt 2) :459-66.Abstract
Voxel based morphometry (VBM) is widely used in the neuroimaging community to infer group differences in brain morphology. VBM is effective in quantifying group differences highly localized in space. However it is not equally effective when group differences might be based on interactions between multiple brain networks. We address this by proposing a new framework called pattern based morphometry (PBM). PBM is a data driven technique. It uses a dictionary learning algorithm to extract global patterns that characterize group differences. We test this approach on simulated and real data obtained from ADNI. In both cases PBM is able to uncover complex global patterns effectively.
Tristán-Vega A, Westin C-F. Probabilistic ODF estimation from reduced HARDI data with sparse regularization. Med Image Comput Comput Assist Interv. 2011;14 (Pt 2) :182-90.Abstract
High Angular Resolution Diffusion Imaging (HARDI) demands a higher amount of data measurements compared to Diffusion Tensor Imaging (DTI), restricting its use in practice. We propose to represent the probabilistic Orientation Distribution Function (ODF) in the frame of Spherical Wavelets (SW), where it is highly sparse. From a reduced subset of measurements (nearly four times less than the standard for HARDI), we pose the estimation as an inverse problem with sparsity regularization. This allows the fast computation of a positive, unit-mass, probabilistic ODF from 14-16 samples, as we show with both synthetic diffusion signals and real HARDI data with typical parameters.
Maddah M, Miller JV, Sullivan EV, Pfefferbaum A, Rohlfing T. Sheet-like white matter fiber tracts: representation, clustering, and quantitative analysis. Med Image Comput Comput Assist Interv. 2011;14 (Pt 2) :191-9.Abstract
We introduce an automated and probabilistic method for subject-specific segmentation of sheet-like fiber tracts. In addition to clustering of trajectories into anatomically meaningful bundles, the method provides statistics of diffusion measures by establishing point correspondences on the estimated medial representation of each bundle. We also introduce a new approach for medial surface generation of sheet-like fiber bundles in order too initialize the proposed clustering algorithm. Applying the new method to a population study of brain aging on 24 subjects demonstrates the capabilities and strengths of the algorithm in identifying and visualizing spatial patterns of group differences.
Rathi Y, Michailovich OV, Setsompop K, Bouix S, Shenton ME, Westin C-F. Sparse Multi-shell Diffusion Imaging. Med Image Comput Comput Assist Interv. 2011;14 (Pt 2) :58-65.Abstract

Diffusion magnetic resonance imaging (dMRI) is an important tool that allows non-invasive investigation of neural architecture of the brain. The data obtained from these in-vivo scans provides important information about the integrity and connectivity of neural fiber bundles in the brain. A multi-shell imaging (MSI) scan can be of great value in the study of several psychiatric and neurological disorders, yet its usability has been limited due to the long acquisition times required. A typical MSI scan involves acquiring a large number of gradient directions for the 2 (or more) spherical shells (several b-values), making the acquisition time significantly long for clinical application. In this work, we propose to use results from the theory of compressive sampling and determine the minimum number of gradient directions required to attain signal reconstruction similar to a traditional MSI scan. In particular, we propose a generalization of the single shell spherical ridgelets basis for sparse representation of multi shell signals. We demonstrate its efficacy on several synthetic and in-vivo data sets and perform quantitative comparisons with solid spherical harmonics based representation. Our preliminary results show that around 20-24 directions per shell are enough for robustly recovering the diffusion propagator.

Kikinis R, Pieper S. 3D Slicer as a tool for interactive brain tumor segmentation. Conf Proc IEEE Eng Med Biol Soc. 2011;2011 :6982-4.Abstract
User interaction is required for reliable segmentation of brain tumors in clinical practice and in clinical research. By incorporating current research tools, 3D Slicer provides a set of interactive, easy to use tools that can be efficiently used for this purpose. One of the modules of 3D Slicer is an interactive editor tool, which contains a variety of interactive segmentation effects. Use of these effects for fast and reproducible segmentation of a single glioblastoma from magnetic resonance imaging data is demonstrated. The innovation in this work lies not in the algorithm, but in the accessibility of the algorithm because of its integration into a software platform that is practical for research in a clinical setting.
Huang J, Gholami B, Agar NYR, Norton I, Haddad WM, Tannenbaum AR. Classification of astrocytomas and oligodendrogliomas from mass spectrometry data using sparse kernel machines. Conf Proc IEEE Eng Med Biol Soc. 2011;2011 :7965-8.Abstract
Glioma histologies are the primary factor in prognostic estimates and are used in determining the proper course of treatment. Furthermore, due to the sensitivity of cranial environments, real-time tumor-cell classification and boundary detection can aid in the precision and completeness of tumor resection. A recent improvement to mass spectrometry known as desorption electrospray ionization operates in an ambient environment without the application of a preparation compound. This allows for a real-time acquisition of mass spectra during surgeries and other live operations. In this paper, we present a framework using sparse kernel machines to determine a glioma sample's histopathological subtype by analyzing its chemical composition acquired by desorption electrospray ionization mass spectrometry.
Gholami B, Agar NYR, Jolesz FA, Haddad WM, Tannenbaum AR. A compressive sensing approach for glioma margin delineation using mass spectrometry. Conf Proc IEEE Eng Med Biol Soc. 2011;2011 :5682-5.Abstract
Surgery, and specifically, tumor resection, is the primary treatment for most patients suffering from brain tumors. Medical imaging techniques, and in particular, magnetic resonance imaging are currently used in diagnosis as well as image-guided surgery procedures. However, studies show that computed tomography and magnetic resonance imaging fail to accurately identify the full extent of malignant brain tumors and their microscopic infiltration. Mass spectrometry is a well-known analytical technique used to identify molecules in a given sample based on their mass. In a recent study, it is proposed to use mass spectrometry as an intraoperative tool for discriminating tumor and non-tumor tissue. Integration of mass spectrometry with the resection module allows for tumor resection and immediate molecular analysis. In this paper, we propose a framework for tumor margin delineation using compressive sensing. Specifically, we show that the spatial distribution of tumor cell concentration can be efficiently reconstructed and updated using mass spectrometry information from the resected tissue. In addition, our proposed framework is model-free, and hence, requires no prior information of spatial distribution of the tumor cell concentration.
Nakhmani A, Tannenbaum A. Particle Filtering with Region-based Matching for Tracking of Partially Occluded and Scaled Targets. SIAM J Imaging Sci. 2011;4 (1) :220-242.Abstract
Visual tracking of arbitrary targets in clutter is important for a wide range of military and civilian applications. We propose a general framework for the tracking of scaled and partially occluded targets, which do not necessarily have prominent features. The algorithm proposed in the present paper utilizes a modified normalized cross-correlation as the likelihood for a particle filter. The algorithm divides the template, selected by the user in the first video frame, into numerous patches. The matching process of these patches by particle filtering allows one to handle the target's occlusions and scaling. Experimental results with fixed rectangular templates show that the method is reliable for videos with nonstationary, noisy, and cluttered background, and provides accurate trajectories in cases of target translation, scaling, and occlusion.
Fedorov A, Li X, Pohl KM, Bouix S, Styner M, Addicott M, Wyatt C, Daunais JB, Wells WM, Kikinis R. Atlas-guided Segmentation of Vervet Monkey Brain MRI. Open Neuroimag J. 2011;5 :186-97.Abstract

The vervet monkey is an important nonhuman primate model that allows the study of isolated environmental factors in a controlled environment. Analysis of monkey MRI often suffers from lower quality images compared with human MRI because clinical equipment is typically used to image the smaller monkey brain and higher spatial resolution is required. This, together with the anatomical differences of the monkey brains, complicates the use of neuroimage analysis pipelines tuned for human MRI analysis. In this paper we developed an open source image analysis framework based on the tools available within the 3D Slicer software to support a biological study that investigates the effect of chronic ethanol exposure on brain morphometry in a longitudinally followed population of male vervets. We first developed a computerized atlas of vervet monkey brain MRI, which was used to encode the typical appearance of the individual brain structures in MRI and their spatial distribution. The atlas was then used as a spatial prior during automatic segmentation to process two longitudinal scans per subject. Our evaluation confirms the consistency and reliability of the automatic segmentation. The comparison of atlas construction strategies reveals that the use of a population-specific atlas leads to improved accuracy of the segmentation for subcortical brain structures. The contribution of this work is twofold. First, we describe an image processing workflow specifically tuned towards the analysis of vervet MRI that consists solely of the open source software tools. Second, we develop a digital atlas of vervet monkey brain MRIs to enable similar studies that rely on the vervet model.

Whitford TJ, Savadjiev P, Kubicki M, O'Donnell LJ, Terry DP, Bouix S, Westin C-F, Schneiderman JS, Bobrow L, Rausch AC, et al. Fiber Geometry in the Corpus Callosum in Schizophrenia: Evidence for Transcallosal Misconnection. Schizophr Res. 2011;132 (1) :69-74.Abstract

BACKGROUND: Structural abnormalities in the callosal fibers connecting the heteromodal association areas of the prefrontal and temporoparietal cortices bilaterally have been suggested to play a role in the etiology of schizophrenia. AIMS: To investigate for geometric abnormalities in these callosal fibers in schizophrenia patients by using a novel Diffusion-Tensor Imaging (DTI) metric of fiber geometry named Shape-Normalized Dispersion (SHD). METHODS: DTIs (3T, 51 gradient directions, 1.7mm isotropic voxels) were acquired from 26 schizophrenia patients and 23 matched healthy controls. The prefrontal and temporoparietal fibers of the corpus callosum were extracted by means of whole-brain tractography, and their mean SHD calculated. RESULTS: The schizophrenia patients exhibited subnormal levels of SHD in the prefrontal callosal fibers when controlling for between-group differences in Fractional Anisotropy. Reduced SHD could reflect either irregularly turbulent or inhomogeneously distributed fiber trajectories in the corpus callosum. CONCLUSIONS: The results suggest that the transcallosal misconnectivity thought to be associated with schizophrenia could reflect abnormalities in fiber geometry. These abnormalities in fiber geometry could potentially be underpinned by neurodevelopmental irregularities.

Langs G, Lashkari D, Sweet A, Tie Y, Rigolo L, Golby AJ, Golland P. Learning an Atlas of a Cognitive Process in its Functional Geometry. Inf Process Med Imaging. 2011;22 :135-46.Abstract

In this paper we construct an atlas that captures functional characteristics of a cognitive process from a population of individuals. The functional connectivity is encoded in a low-dimensional embedding space derived from a diffusion process on a graph that represents correlations of fMRI time courses. The atlas is represented by a common prior distribution for the embedded fMRI signals of all subjects. The atlas is not directly coupled to the anatomical space, and can represent functional networks that are variable in their spatial distribution. We derive an algorithm for fitting this generative model to the observed data in a population. Our results in a language fMRI study demonstrate that the method identifies coherent and functionally equivalent regions across subjects.

Risholm P, Fedorov A, Pursley J, Tuncali K, Cormack R, Wells WM. Probabilistic Non-rigid Registration of Prostate Images: Modeling and Quantifying Uncertainty. Proc IEEE Int Symp Biomed Imaging. 2011;2011 :553-6.Abstract

Registration of pre- to intra-procedural prostate images needs to handle the large changes in position and shape of the prostate caused by varying rectal filling and patient positioning. We describe a probabilistic method for non-rigid registration of prostate images which can quantify the most probable deformation as well as the uncertainty of the estimated deformation. The method is based on a biomechanical Finite Element model which treats the prostate as an elastic material. We use a Markov Chain Monte Carlo sampler to draw deformation configurations from the posterior distribution. In practice, we simultaneously estimate the boundary conditions (surface displacements) and the internal deformations of our biomechanical model. The proposed method was validated on a clinical MRI dataset with registration results comparable to previously published methods, but with the added benefit of also providing uncertainty estimates which may be important to take into account during prostate biopsy and brachytherapy procedures.

Janoos F, Singh S, Machiraju R, Wells III WM, Mórocz IA. State-space Models of Mental Processes from fMRI. Inf Process Med Imaging. 2011;22 :588-99.Abstract

In addition to functional localization and integration, the problem of determining whether the data encode some information about the mental state of the subject, and if so, how this information is represented has become an important research agenda in functional neuroimaging. Multivariate classifiers, commonly used for brain state decoding, are restricted to simple experimental paradigms with a fixed number of alternatives and are limited in their representation of the temporal dimension of the task. Moreover, they learn a mapping from the data to experimental conditions and therefore do not explain the intrinsic patterns in the data. In this paper, we present a data-driven approach to building a spatio-temporal representation of mental processes using a state-space formalism, without reference to experimental conditions. Efficient Monte Carlo algorithms for estimating the parameters of the model along with a method for model-size selection are developed. The advantages of such a model in determining the mental-state of the subject over pattern classifiers are demonstrated using an fMRI study of mental arithmetic.

Pages