Publications by Year: 2012


Matthew Toews, William M Wells, and Lilla Zöllei. 2012. A Feature-based Developmental Model of the Infant Brain in Structural MRI. Med Image Comput Comput Assist Interv, 15, Pt 2, Pp. 204-11.
In this paper, anatomical development is modeled as a collection of distinctive image patterns localized in space and time. A Bayesian posterior probability is defined over a random variable of subject age, conditioned on data in the form of scale-invariant image features. The model is automatically learned from a large set of images exhibiting significant variation, used to discover anatomical structure related to age and development, and fit to new images to predict age. The model is applied to a set of 230 infant structural MRIs of 92 subjects acquired at multiple sites over an age range of 8-590 days. Experiments demonstrate that the model can be used to identify age-related anatomical structure, and to predict the age of new subjects with an average error of 72 days.
Jan Egger, Tina Kapur, Christopher Nimsky, and Ron Kikinis. 2012. Pituitary adenoma volumetry with 3D Slicer. PLoS One, 7, 12, Pp. e51788.
In this study, we present pituitary adenoma volumetry using the free and open source medical image computing platform for biomedical research: (3D) Slicer. Volumetric changes in cerebral pathologies like pituitary adenomas are a critical factor in treatment decisions by physicians and in general the volume is acquired manually. Therefore, manual slice-by-slice segmentations in magnetic resonance imaging (MRI) data, which have been obtained at regular intervals, are performed. In contrast to this manual time consuming slice-by-slice segmentation process Slicer is an alternative which can be significantly faster and less user intensive. In this contribution, we compare pure manual segmentations of ten pituitary adenomas with semi-automatic segmentations under Slicer. Thus, physicians drew the boundaries completely manually on a slice-by-slice basis and performed a Slicer-enhanced segmentation using the competitive region-growing based module of Slicer named GrowCut. Results showed that the time and user effort required for GrowCut-based segmentations were on average about thirty percent less than the pure manual segmentations. Furthermore, we calculated the Dice Similarity Coefficient (DSC) between the manual and the Slicer-based segmentations to proof that the two are comparable yielding an average DSC of 81.97±3.39%.
Liangjia Zhu, Yi Gao, Anthony Yezzi, Rob MacLeod, Joshua Cates, and Allen Tannenbaum. 2012. Automatic segmentation of the left atrium from MRI images using salient feature and contour evolution. Conf Proc IEEE Eng Med Biol Soc, 2012, Pp. 3211-4.
We propose an automatic approach for segmenting the left atrium from MRI images. In particular, the thoracic aorta is detected and used as a salient feature to find a seed region that lies inside the left atrium. A hybrid energy that combines robust statistics and localized region intensity information is employed to evolve active contours from the seed region to capture the whole left atrium. The experimental results demonstrate the accuracy and robustness of our approach.
Ofer Pasternak, Martha E Shenton, and Carl-Fredrik Westin. 2012. Estimation of extracellular volume from regularized multi-shell diffusion MRI. Med Image Comput Comput Assist Interv, 15, Pt 2, Pp. 305-12.
Diffusion MRI measures micron scale displacement of water molecules, providing unique insight into microstructural tissue architecture. However, current practical image resolution is in the millimeter scale, and thus diffusivities from many tissue compartments are averaged in each voxel, reducing the sensitivity and specificity of the measurement to subtle pathologies. Recent studies have pointed out that eliminating the contribution of extracellular water increases the sensitivity of the diffusion measures to tissue architecture. Moreover, in brain imaging, estimation of the extracellular volume appears to indicate pathological processes such as atrophy, edema and neuroinflammation. Here we study the free-water method, which assumes a bi-tensor model. We add low b-value shells to a regular DTI acquisition and present methods to improve the estimation of the model parameters using the extra information. In addition, we define a Laplace-Beltrami regularization operator that further stabilizes the multi-shell estimation.
Archana Venkataraman, Marek Kubicki, and Polina Golland. 2012. From brain connectivity models to identifying foci of a neurological disorder. Med Image Comput Comput Assist Interv, 15, Pt 1, Pp. 715-22.
We propose a novel approach to identify the foci of a neurological disorder based on anatomical and functional connectivity information. Specifically, we formulate a generative model that characterizes the network of abnormal functional connectivity emanating from the affected foci. We employ the variational EM algorithm to fit the model and to identify both the afflicted regions and the differences in connectivity induced by the disorder. We demonstrate our method on a population study of schizophrenia.
Yi Gao, Zhuo Li, Ziyin Lin, Liangjia Zhu, Allen Tannenbaum, Sylvain Bouix, and C P Wong. 2012. Automated dispersion and orientation analysis for carbon nanotube reinforced polymer composites. Nanotechnology, 23, 43, Pp. 435706.
The properties of carbon nanotube (CNT)/polymer composites are strongly dependent on the dispersion and orientation of CNTs in the host matrix. Quantification of the dispersion and orientation of CNTs by means of microstructure observation and image analysis has been demonstrated as a useful way to understand the structure-property relationship of CNT/polymer composites. However, due to the various morphologies and large amount of CNTs in one image, automatic and accurate identification of CNTs has become the bottleneck for dispersion/orientation analysis. To solve this problem, shape identification is performed for each pixel in the filler identification step, so that individual CNTs can be extracted from images automatically. The improved filler identification enables more accurate analysis of CNT dispersion and orientation. The dispersion index and orientation index obtained for both synthetic and real images from model compounds correspond well with the observations. Moreover, these indices help to explain the electrical properties of CNT/silicone composite, which is used as a model compound. This method can also be extended to other polymer composites with high-aspect-ratio fillers.
Ofer Pasternak, Carl-Fredrik Westin, Sylvain Bouix, Larry J Seidman, Jill M Goldstein, Tsung-Ung W Woo, Tracey L Petryshen, Raquelle I Mesholam-Gately, Robert W McCarley, Ron Kikinis, Martha E Shenton, and Marek Kubicki. 2012. Excessive extracellular volume reveals a neurodegenerative pattern in schizophrenia onset. J Neurosci, 32, 48, Pp. 17365-72.
Diffusion MRI has been successful in identifying the existence of white matter abnormalities in schizophrenia in vivo. However, the role of these abnormalities in the etiology of schizophrenia is not well understood. Accumulating evidence from imaging, histological, genetic, and immunochemical studies support the involvement of axonal degeneration and neuroinflammation—ubiquitous components of neurodegenerative disorders—as the underlying pathologies of these abnormalities. Nevertheless, the current imaging modalities cannot distinguish neuroinflammation from axonal degeneration, and therefore provide little specificity with respect to the pathophysiology progression and whether it is related to a neurodegenerative process. Free-water imaging is a new methodology that is sensitive to water molecules diffusing in the extracellular space. Excessive extracellular volume is a surrogate biomarker for neuroinflammation and can be separated out to reveal abnormalities such as axonal degeneration that affect diffusion characteristics in the tissue. We applied free-water imaging on diffusion MRI data acquired from schizophrenia-diagnosed human subjects with a first psychotic episode. We found a significant increase in the extracellular volume in both white and gray matter. In contrast, significant signs of axonal degeneration were limited to focal areas in the frontal lobe white matter. Our findings demonstrate that neuroinflammation is more prominent than axonal degeneration in the early stage of schizophrenia, revealing a pattern shared by many neurodegenerative disorders, in which prolonged inflammation leads to axonal degeneration. These findings promote anti-inflammatory treatment for early diagnosed schizophrenia patients.
Robert J Cooper, Matteo Caffini, Jay Dubb, Qianqian Fang, Anna Custo, Daisuke Tsuzuki, Bruce Fischl, William Wells, Ippeita Dan, and David A Boas. 2012. Validating atlas-guided DOT: a comparison of diffuse optical tomography informed by atlas and subject-specific anatomies. Neuroimage, 62, 3, Pp. 1999-2006.
We describe the validation of an anatomical brain atlas approach to the analysis of diffuse optical tomography (DOT). Using MRI data from 32 subjects, we compare the diffuse optical images of simulated cortical activation reconstructed using a registered atlas with those obtained using a subject’s true anatomy. The error in localization of the simulated cortical activations when using a registered atlas is due to a combination of imperfect registration, anatomical differences between atlas and subject anatomies and the localization error associated with diffuse optical image reconstruction. When using a subject-specific MRI, any localization error is due to diffuse optical image reconstruction only. In this study we determine that using a registered anatomical brain atlas results in an average localization error of approximately 18 mm in Euclidean space. The corresponding error when the subject’s own MRI is employed is 9.1 mm. In general, the cost of using atlas-guided DOT in place of subject-specific MRI-guided DOT is a doubling of the localization error. Our results show that despite this increase in error, reasonable anatomical localization is achievable even in cases where the subject-specific anatomy is unavailable.
Yi Gao, Yogesh Rathi, Sylvain Bouix, and Allen Tannenbaum. 2012. Filtering in the diffeomorphism group and the registration of point sets. IEEE Trans Image Process, 21, 10, Pp. 4383-96.
The registration of a pair of point sets as well as the estimation of their pointwise correspondences is a challenging and important task in computer vision. In this paper, we present a method to estimate the diffeomorphic deformation, together with the pointwise correspondences, between a pair of point sets. Many of the registration problems are iteratively solved by estimating the correspondence, locally optimizing certain cost functionals over the rigid or similarity or affine transformation group, then estimating the correspondence again, and so on. This type of approach, however, is well-known to be susceptible to suboptimal local solutions. In this paper, we first adopt the perspective of treating the registration as a posterior estimation optimization problem and solve it accordingly via a particle-filtering framework. Second, within such a framework, the diffeomorphic registration is performed to correct the nonlinear deformation of the points. In doing so, we provide a solution less susceptible to local minima. We provide the experimental results, which include challenging medical data sets where the two point sets differ by 180 (°) rotation as well as local deformations, to highlight the algorithm’s capability of robustly finding the more globally optimal solution for the registration task.
Zora Kikinis, Takeshi Asami, Sylvain Bouix, C T Finn, Thomas Ballinger, Erica Tworog-Dube, Raju Kucherlapati, Ron Kikinis, Martha E Shenton, and Marek Kubicki. 2012. Reduced Fractional Anisotropy and Axial Diffusivity in White Matter in 22q11.2 Deletion Syndrome: A Pilot Study. Schizophr Res, 141, 1, Pp. 35-9.
Individuals with 22q11.2 deletion syndrome (22q11.2DS) evince a 30% incidence of schizophrenia. We compared the white matter (WM) of 22q11.2DS patients without schizophrenia to a group of matched healthy controls using Tract-Based-Spatial-Statistics (TBSS). We found localized reduction of Fractional Anisotropy (FA) and Axial Diffusivity (AD; measure of axonal integrity) in WM underlying the left parietal lobe. No changes in Radial Diffusivity (RD; measure of myelin integrity) were observed. Of note, studies in chronic schizophrenia patients report reduced FA, no changes in AD, and increases in RD in WM. Our findings suggest different WM microstructural pathology in 22q11.2DS than in patients with schizophrenia.