Publications by Year: 2011


Rathi Y, Kubicki M, Bouix S, Westin CF, Goldstein J, Seidman L, Mesholam-Gately R, McCarley RW, Shenton ME. Statistical Analysis of Fiber Bundles using Multi-tensor Tractography: Application to First-episode Schizophrenia. Magn Reson Imaging. 2011;29(4):507–15.
This work proposes a new method to detect abnormalities in fiber bundles of first-episode (FE) schizophrenia patients. Existing methods have either examined a particular region of interest or used voxel-based morphometry or used tracts generated using the single tensor model for locating statistically different fiber bundles. Further, a two-sample t test, which assumes a Gaussian distribution for each population, is the most widely used statistical hypothesis testing algorithm. In this study, we use the unscented Kalman filter based two-tensor tractography algorithm for tracing neural fiber bundles of the brain that connect 105 different cortical and subcortical regions. Next, fiber bundles with significant connectivity across the entire population were determined. Several diffusion measures derived from the two-tensor model were computed and used as features in the subsequent analysis. For each fiber bundle, an affine-invariant descriptor was computed, thus obviating the need for precise registration of patients to an atlas. A kernel-based statistical hypothesis testing algorithm, which makes no assumption regarding the distribution of the underlying population, was then used to determine the abnormal diffusion properties of all fiber bundles for 20 FE patients and 20 age-matched healthy controls. Of the 1254 fiber bundles with significant connectivity, 740 fiber bundles were found to be significantly different in at least one diffusion measure after correcting for multiple comparisons. Thus, the changes affecting first-episode patients seem to be global in nature (spread throughout the brain).
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.
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.
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 WM III, Mórocz IA. State-space Models of Mental Processes from fMRI. Inf Process Med Imaging. 2011;22:588–99.
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.
Whitford TJ, Savadjiev P, Kubicki M, Donnell LJO, Terry DP, Bouix S, Westin CF, Schneiderman JS, Bobrow L, Rausch AC, Niznikiewicz M, Nestor PG, Pantelis C, Wood SJ, McCarley RW, Shenton ME. Fiber Geometry in the Corpus Callosum in Schizophrenia: Evidence for Transcallosal Misconnection. Schizophr Res. 2011;132(1):69–74.
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.
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.
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.
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.
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.
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.
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.
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.