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Muralidharan P, Fishbaugh J, Johnson HJ, Durrleman S, Paulsen JS, Gerig G, Fletcher PT. Diffeomorphic shape trajectories for improved longitudinal segmentation and statistics. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2014; 17:49-56. [PMID: 25320781 PMCID: PMC4486086 DOI: 10.1007/978-3-319-10443-0_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
Longitudinal imaging studies involve tracking changes in individuals by repeated image acquisition over time. The goal of these studies is to quantify biological shape variability within and across individuals, and also to distinguish between normal and disease populations. However, data variability is influenced by outside sources such as image acquisition, image calibration, human expert judgment, and limited robustness of segmentation and registration algorithms. In this paper, we propose a two-stage method for the statistical analysis of longitudinal shape. In the first stage, we estimate diffeomorphic shape trajectories for each individual that minimize inconsistencies in segmented shapes across time. This is followed by a longitudinal mixed-effects statistical model in the second stage for testing differences in shape trajectories between groups. We apply our method to a longitudinal database from PREDICT-HD and demonstrate our approach reduces unwanted variability for both shape and derived measures, such as volume. This leads to greater statistical power to distinguish differences in shape trajectory between healthy subjects and subjects with a genetic biomarker for Huntington's disease (HD).
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Hao X, Zygmunt K, Whitaker RT, Fletcher PT. Improved segmentation of white matter tracts with adaptive Riemannian metrics. Med Image Anal 2014; 18:161-75. [PMID: 24211814 PMCID: PMC3898892 DOI: 10.1016/j.media.2013.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 09/23/2013] [Accepted: 10/15/2013] [Indexed: 10/26/2022]
Abstract
We present a novel geodesic approach to segmentation of white matter tracts from diffusion tensor imaging (DTI). Compared to deterministic and stochastic tractography, geodesic approaches treat the geometry of the brain white matter as a manifold, often using the inverse tensor field as a Riemannian metric. The white matter pathways are then inferred from the resulting geodesics, which have the desirable property that they tend to follow the main eigenvectors of the tensors, yet still have the flexibility to deviate from these directions when it results in lower costs. While this makes such methods more robust to noise, the choice of Riemannian metric in these methods is ad hoc. A serious drawback of current geodesic methods is that geodesics tend to deviate from the major eigenvectors in high-curvature areas in order to achieve the shortest path. In this paper we propose a method for learning an adaptive Riemannian metric from the DTI data, where the resulting geodesics more closely follow the principal eigenvector of the diffusion tensors even in high-curvature regions. We also develop a way to automatically segment the white matter tracts based on the computed geodesics. We show the robustness of our method on simulated data with different noise levels. We also compare our method with tractography methods and geodesic approaches using other Riemannian metrics and demonstrate that the proposed method results in improved geodesics and segmentations using both synthetic and real DTI data.
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Sadeghi N, Fletcher PT, Prastawa M, Gilmore JH, Gerig G. Subject-specific prediction using nonlinear population modeling: application to early brain maturation from DTI. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2014; 17:33-40. [PMID: 25320779 DOI: 10.1007/978-3-319-10443-0_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The term prediction implies expected outcome in the future, often based on a model and statistical inference. Longitudinal imaging studies offer the possibility to model temporal change trajectories of anatomy across populations of subjects. In the spirit of subject-specific analysis, such normative models can then be used to compare data from new subjects to the norm and to study progression of disease or to predict outcome. This paper follows a statistical inference approach and presents a framework for prediction of future observations based on past measurements and population statistics. We describe prediction in the context of nonlinear mixed effects modeling (NLME) where the full reference population's statistics (estimated fixed effects, variance-covariance of random effects, variance of noise) is used along with the individual's available observations to predict its trajectory. The proposed methodology is generic in regard to application domains. Here, we demonstrate analysis of early infant brain maturation from longitudinal DTI with up to three time points. Growth as observed in DTI-derived scalar invariants is modeled with a parametric function, its parameters being input to NLME population modeling. Trajectories of new subject's data are estimated when using no observation, only the first or the first two time points. Leave-one-out experiments result in statistics on differences between actual and predicted observations. We also simulate a clinical scenario of prediction on multiple categories, where trajectories predicted from multiple models are classified based on maximum likelihood criteria.
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Yu YY, Fletcher PT, Awate SP. Hierarchical bayesian modeling, estimation, and sampling for multigroup shape analysis. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2014; 17:9-16. [PMID: 25320776 PMCID: PMC4872874 DOI: 10.1007/978-3-319-10443-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
This paper proposes a novel method for the analysis of anatomical shapes present in biomedical image data. Motivated by the natural organization of population data into multiple groups, this paper presents a novel hierarchical generative statistical model on shapes. The proposed method represents shapes using pointsets and defines a joint distribution on the population's (i) shape variables and (ii) object-boundary data. The proposed method solves for optimal (i) point locations, (ii) correspondences, and (iii) model-parameter values as a single optimization problem. The optimization uses expectation maximization relying on a novel Markov-chain Monte-Carlo algorithm for sampling in Kendall shape space. Results on clinical brain images demonstrate advantages over the state of the art.
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Sharma A, Fletcher PT, Gilmore JH, Escolar ML, Gupta A, Styner M, Gerig G. SPATIOTEMPORAL MODELING OF DISCRETE-TIME DISTRIBUTION-VALUED DATA APPLIED TO DTI TRACT EVOLUTION IN INFANT NEURODEVELOPMENT. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2013; 2013:684-687. [PMID: 24443688 DOI: 10.1109/isbi.2013.6556567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This paper proposes a novel method that extends spatiotemporal growth modeling to distribution-valued data. The method relaxes assumptions on the underlying noise models by considering the data to be represented by the complete probability distributions rather than a representative, single-valued summary statistics like the mean. When summarizing by the latter method, information on the underlying variability of data is lost early in the process and is not available at later stages of statistical analysis. The concept of 'distance' between distributions and an 'average' of distributions is employed. The framework quantifies growth trajectories for individuals and populations in terms of the complete data variability estimated along time and space. Concept is demonstrated in the context of our driving application which is modeling of age-related changes along white matter tracts in early neurodevelopment. Results are shown for a single subject with Krabbe's disease in comparison with a normative trend estimated from 15 healthy controls.
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Nielsen JA, Zielinski BA, Fletcher PT, Alexander AL, Lange N, Bigler ED, Lainhart JE, Anderson JS. Multisite functional connectivity MRI classification of autism: ABIDE results. Front Hum Neurosci 2013; 7:599. [PMID: 24093016 PMCID: PMC3782703 DOI: 10.3389/fnhum.2013.00599] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 09/04/2013] [Indexed: 12/02/2022] Open
Abstract
Background: Systematic differences in functional connectivity MRI metrics have been consistently observed in autism, with predominantly decreased cortico-cortical connectivity. Previous attempts at single subject classification in high-functioning autism using whole brain point-to-point functional connectivity have yielded about 80% accurate classification of autism vs. control subjects across a wide age range. We attempted to replicate the method and results using the Autism Brain Imaging Data Exchange (ABIDE) including resting state fMRI data obtained from 964 subjects and 16 separate international sites. Methods: For each of 964 subjects, we obtained pairwise functional connectivity measurements from a lattice of 7266 regions of interest covering the gray matter (26.4 million “connections”) after preprocessing that included motion and slice timing correction, coregistration to an anatomic image, normalization to standard space, and voxelwise removal by regression of motion parameters, soft tissue, CSF, and white matter signals. Connections were grouped into multiple bins, and a leave-one-out classifier was evaluated on connections comprising each set of bins. Age, age-squared, gender, handedness, and site were included as covariates for the classifier. Results: Classification accuracy significantly outperformed chance but was much lower for multisite prediction than for previous single site results. As high as 60% accuracy was obtained for whole brain classification, with the best accuracy from connections involving regions of the default mode network, parahippocampaland fusiform gyri, insula, Wernicke Area, and intraparietal sulcus. The classifier score was related to symptom severity, social function, daily living skills, and verbal IQ. Classification accuracy was significantly higher for sites with longer BOLD imaging times. Conclusions: Multisite functional connectivity classification of autism outperformed chance using a simple leave-one-out classifier, but exhibited poorer accuracy than for single site results. Attempts to use multisite classifiers will likely require improved classification algorithms, longer BOLD imaging times, and standardized acquisition parameters for possible future clinical utility.
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Duffield T, Trontel H, Bigler ED, Froehlich A, Prigge MB, Travers B, Green RR, Cariello AN, Cooperrider J, Nielsen J, Alexander A, Anderson J, Fletcher PT, Lange N, Zielinski B, Lainhart J. Neuropsychological investigation of motor impairments in autism. J Clin Exp Neuropsychol 2013; 35:867-81. [PMID: 23985036 PMCID: PMC3907511 DOI: 10.1080/13803395.2013.827156] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It is unclear how standardized neuropsychological measures of motor function relate to brain volumes of motor regions in autism spectrum disorder (ASD). An all-male sample composed of 59 ASD and 30 controls (ages 5-33 years) completed three measures of motor function: strength of grip (SOG), finger tapping test (FTT), and grooved pegboard test (GPT). Likewise, all participants underwent magnetic resonance imaging with region of interest (ROI) volumes obtained to include the following regions: motor cortex (precentral gyrus), somatosensory cortex (postcentral gyrus), thalamus, basal ganglia, cerebellum, and caudal middle frontal gyrus. These traditional neuropsychological measures of motor function are assumed to differ in motor complexity, with GPT requiring the most followed by FTT and SOG. Performance by ASD participants on the GPT and FTT differed significantly from that of controls, with the largest effect size differences observed on the more complex GPT task. Differences on the SOG task between the two groups were nonsignificant. Since more complex motor tasks tap more complex networks, poorer GPT performance by those with ASD may reflect less efficient motor networks. There was no gross pathology observed in classic motor areas of the brain in ASD, as ROI volumes did not differ, but FTT was negatively related to motor cortex volume in ASD. The results suggest a hierarchical motor disruption in ASD, with difficulties evident only in more complex tasks as well as a potential anomalous size-function relation in motor cortex in ASD.
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Singh N, Hinkle J, Joshi S, Fletcher PT. A VECTOR MOMENTA FORMULATION OF DIFFEOMORPHISMS FOR IMPROVED GEODESIC REGRESSION AND ATLAS CONSTRUCTION. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2013; 2013:1219-1222. [PMID: 25404997 DOI: 10.1109/isbi.2013.6556700] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This paper presents a novel approach for diffeomorphic image regression and atlas estimation that results in improved convergence and numerical stability. We use a vector momenta representation of a diffeomorphism's initial conditions instead of the standard scalar momentum that is typically used. The corresponding variational problem results in a closed-form update for template estimation in both the geodesic regression and atlas estimation problems. While we show that the theoretical optimal solution is equivalent to the scalar momenta case, the simplification of the optimization problem leads to more stable and efficient estimation in practice. We demonstrate the effectiveness of our method for atlas estimation and geodesic regression using synthetically generated shapes and 3D MRI brain scans.
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Prigge MD, Bigler ED, Fletcher PT, Zielinski BA, Ravichandran C, Anderson J, Froehlich A, Abildskov T, Papadopolous E, Maasberg K, Nielsen JA, Alexander AL, Lange N, Lainhart J. Longitudinal Heschl's gyrus growth during childhood and adolescence in typical development and autism. Autism Res 2013; 6:78-90. [PMID: 23436773 PMCID: PMC3669648 DOI: 10.1002/aur.1265] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/29/2012] [Indexed: 11/07/2022]
Abstract
Heightened auditory sensitivity and atypical auditory processing are common in autism. Functional studies suggest abnormal neural response and hemispheric activation to auditory stimuli, yet the neurodevelopment underlying atypical auditory function in autism is unknown. In this study, we model longitudinal volumetric growth of Heschl's gyrus gray matter and white matter during childhood and adolescence in 40 individuals with autism and 17 typically developing participants. Up to three time points of magnetic resonance imaging data, collected on average every 2.5 years, were examined from individuals 3-12 years of age at the time of their first scan. Consistent with previous cross-sectional studies, no group differences were found in Heschl's gyrus gray matter volume or asymmetry. However, reduced longitudinal gray matter volumetric growth was found in the right Heschl's gyrus in autism. Reduced longitudinal white matter growth in the left hemisphere was found in the right-handed autism participants. Atypical Heschl's gyrus white matter volumetric growth was found bilaterally in the autism individuals with a history of delayed onset of spoken language. Heightened auditory sensitivity, obtained from the Sensory Profile, was associated with reduced volumetric gray matter growth in the right hemisphere. Our longitudinal analyses revealed dynamic gray and white matter changes in Heschl's gyrus throughout childhood and adolescence in both typical development and autism.
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Cardenas VA, Tosun D, Chao LL, Fletcher PT, Joshi S, Weiner MW, Schuff N. Voxel-wise co-analysis of macro- and microstructural brain alteration in mild cognitive impairment and Alzheimer's disease using anatomical and diffusion MRI. J Neuroimaging 2013; 24:435-43. [PMID: 23421601 DOI: 10.1111/jon.12002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 10/01/2012] [Accepted: 10/28/2012] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND PURPOSE To determine if a voxel-wise "co-analysis" of structural and diffusion tensor magnetic resonance imaging (MRI) together reveals additional brain regions affected in mild cognitive impairment (MCI) and Alzheimer's disease (AD) than voxel-wise analysis of the individual MRI modalities alone. METHODS Twenty-one patients with MCI, 21 patients with AD, and 21 cognitively normal healthy elderly were studied with MRI. Maps of deformation and fractional anisotropy (FA) were computed and used as dependent variables in univariate and multivariate statistical models. RESULTS Univariate voxel-wise analysis of macrostructural changes in MCI showed atrophy in the right anterior temporal lobe, left posterior parietal/precuneus region, WM adjacent to the cingulate gyrus, and dorsolateral prefrontal regions, consistent with prior research. Univariate voxel-wise analysis of microstructural changes in MCI showed reduced FA in the left posterior parietal region extending into the corpus callosum, consistent with previous work. The multivariate analysis, which provides more information than univariate tests when structural and FA measures are correlated, revealed additional MCI-related changes in corpus callosum and temporal lobe. CONCLUSION These results suggest that in corpus callosum and temporal regions macro- and microstructural variations in MCI can be congruent, providing potentially new insight into the mechanisms of brain tissue degeneration.
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Sadeghi N, Prastawa M, Fletcher PT, Vachet C, Wang B, Gilmore J, Gerig G. MULTIVARIATE MODELING OF LONGITUDINAL MRI IN EARLY BRAIN DEVELOPMENT WITH CONFIDENCE MEASURES. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2013:1400-1403. [PMID: 23959506 PMCID: PMC3744330 DOI: 10.1109/isbi.2013.6556795] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The human brain undergoes rapid organization and structuring early in life. Longitudinal imaging enables the study of these changes over a developmental period within individuals through estimation of population growth trajectory and its variability. In this paper, we focus on maturation of white and gray matter depicted in structural and diffusion MRI of healthy subjects with repeated scans. We provide a framework for joint analysis of both structural MRI and DTI (Diffusion Tensor Imaging) using multivariate nonlinear mixed effect modeling of temporal changes. Our framework constructs normative growth models for all the modalities, taking into account the correlation among the modalities and individuals, along with estimation of the variability of the population trends. We apply our method to study early brain development, and to our knowledge this is the first multimodel longitudinal modeling of diffusion and signal intensity changes for this growth stage. Results show the potential of our framework to study growth trajectories, as well as neurodevelopmental disorders through comparison against the constructed normative models of multimodal 4D MRI.
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Singh N, Hinkle J, Joshi S, Fletcher PT. A hierarchical geodesic model for diffeomorphic longitudinal shape analysis. INFORMATION PROCESSING IN MEDICAL IMAGING : PROCEEDINGS OF THE ... CONFERENCE 2013; 23:560-71. [PMID: 24683999 PMCID: PMC6400284 DOI: 10.1007/978-3-642-38868-2_47] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Hierarchical linear models (HLMs) are a standard approach for analyzing data where individuals are measured repeatedly over time. However, such models are only applicable to longitudinal studies of Euclidean data. In this paper, we propose a novel hierarchical geodesic model (HGM), which generalizes HLMs to the manifold setting. Our proposed model explains the longitudinal trends in shapes represented as elements of the group of diffeomorphisms. The individual level geodesics represent the trajectory of shape changes within individuals. The group level geodesic represents the average trajectory of shape changes for the population. We derive the solution of HGMs on diffeomorphisms to estimate individual level geodesics, the group geodesic, and the residual geodesics. We demonstrate the effectiveness of HGMs for longitudinal analysis of synthetically generated shapes and 3D MRI brain scans.
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Zhu X, Gur Y, Wang W, Fletcher PT. Model selection and estimation of multi-compartment models in diffusion MRI with a Rician noise model. INFORMATION PROCESSING IN MEDICAL IMAGING : PROCEEDINGS OF THE ... CONFERENCE 2013; 23:644-55. [PMID: 24684006 PMCID: PMC6400282 DOI: 10.1007/978-3-642-38868-2_54] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Multi-compartment models in diffusion MRI (dMRI) are used to describe complex white matter fiber architecture of the brain. In this paper, we propose a novel multi-compartment estimation method based on the ball-and-stick model, which is composed of an isotropic diffusion compartment ("ball") as well as one or more perfectly linear diffusion compartments ("sticks"). To model the noise distribution intrinsic to dMRI measurements, we introduce a Rician likelihood term and estimate the model parameters by means of an Expectation Maximization (EM) algorithm. This paper also addresses the problem of selecting the number of fiber compartments that best fit the data, by introducing a sparsity prior on the volume mixing fractions. This term provides automatic model selection and enables us to discriminate different fiber populations. When applied to simulated data, our method provides accurate estimates of the fiber orientations, diffusivities, and number of compartments, even at low SNR, and outperforms similar methods that rely on a Gaussian noise distribution assumption. We also apply our method to in vivo brain data and show that it can successfully capture complex fiber structures that match the known anatomy.
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Sadeghi N, Prastawa M, Fletcher PT, Wolff J, Gilmore JH, Gerig G. Regional characterization of longitudinal DT-MRI to study white matter maturation of the early developing brain. Neuroimage 2012; 68:236-47. [PMID: 23235270 DOI: 10.1016/j.neuroimage.2012.11.040] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/21/2012] [Accepted: 11/15/2012] [Indexed: 10/27/2022] Open
Abstract
The human brain undergoes rapid and dynamic development early in life. Assessment of brain growth patterns relevant to neurological disorders and disease requires a normative population model of growth and variability in order to evaluate deviation from typical development. In this paper, we focus on maturation of brain white matter as shown in diffusion tensor MRI (DT-MRI), measured by fractional anisotropy (FA), mean diffusivity (MD), as well as axial and radial diffusivities (AD, RD). We present a novel methodology to model temporal changes of white matter diffusion from longitudinal DT-MRI data taken at discrete time points. Our proposed framework combines nonlinear modeling of trajectories of individual subjects, population analysis, and testing for regional differences in growth pattern. We first perform deformable mapping of longitudinal DT-MRI of healthy infants imaged at birth, 1 year, and 2 years of age, into a common unbiased atlas. An existing template of labeled white matter regions is registered to this atlas to define anatomical regions of interest. Diffusivity properties of these regions, presented over time, serve as input to the longitudinal characterization of changes. We use non-linear mixed effect (NLME) modeling where temporal change is described by the Gompertz function. The Gompertz growth function uses intuitive parameters related to delay, rate of change, and expected asymptotic value; all descriptive measures which can answer clinical questions related to quantitative analysis of growth patterns. Results suggest that our proposed framework provides descriptive and quantitative information on growth trajectories that can be interpreted by clinicians using natural language terms that describe growth. Statistical analysis of regional differences between anatomical regions which are known to mature differently demonstrates the potential of the proposed method for quantitative assessment of brain growth and differences thereof. This will eventually lead to a prediction of white matter diffusion properties and associated cognitive development at later stages given imaging data at early stages.
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Zielinski BA, Anderson JS, Froehlich AL, Prigge MBD, Nielsen JA, Cooperrider JR, Cariello AN, Fletcher PT, Alexander AL, Lange N, Bigler ED, Lainhart JE. scMRI reveals large-scale brain network abnormalities in autism. PLoS One 2012. [PMID: 23185305 PMCID: PMC3504046 DOI: 10.1371/journal.pone.0049172] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Autism is a complex neurological condition characterized by childhood onset of dysfunction in multiple cognitive domains including socio-emotional function, speech and language, and processing of internally versus externally directed stimuli. Although gross brain anatomic differences in autism are well established, recent studies investigating regional differences in brain structure and function have yielded divergent and seemingly contradictory results. How regional abnormalities relate to the autistic phenotype remains unclear. We hypothesized that autism exhibits distinct perturbations in network-level brain architecture, and that cognitive dysfunction may be reflected by abnormal network structure. Network-level anatomic abnormalities in autism have not been previously described. We used structural covariance MRI to investigate network-level differences in gray matter structure within two large-scale networks strongly implicated in autism, the salience network and the default mode network, in autistic subjects and age-, gender-, and IQ-matched controls. We report specific perturbations in brain network architecture in the salience and default-mode networks consistent with clinical manifestations of autism. Extent and distribution of the salience network, involved in social-emotional regulation of environmental stimuli, is restricted in autism. In contrast, posterior elements of the default mode network have increased spatial distribution, suggesting a ‘posteriorization’ of this network. These findings are consistent with a network-based model of autism, and suggest a unifying interpretation of previous work. Moreover, we provide evidence of specific abnormalities in brain network architecture underlying autism that are quantifiable using standard clinical MRI.
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Datar M, Muralidharan P, Kumar A, Gouttard S, Piven J, Gerig G, Whitaker R, Fletcher PT. Mixed-Effects Shape Models for Estimating Longitudinal Changes in Anatomy. SPATIO-TEMPORAL IMAGE ANALYSIS FOR LONGITUDINAL AND TIME-SERIES IMAGE DATA : SECOND INTERNATIONAL WORKSHOP, STIA 2012, HELD IN CONJUNCTION WITH MICCAI 2012, NICE, FRANCE, OCTOBER 1, 2012, PROCEEDINGS. STIA (CONFERENCE) (2ND : 2012 : NIC... 2012; 7570:76-87. [PMID: 25506622 DOI: 10.1007/978-3-642-33555-6_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this paper, we propose a new method for longitudinal shape analysis that fits a linear mixed-effects model, while simultaneously optimizing correspondences on a set of anatomical shapes. Shape changes are modeled in a hierarchical fashion, with the global population trend as a fixed effect and individual trends as random effects. The statistical significance of the estimated trends are evaluated using specifically designed permutation tests. We also develop a permutation test based on the Hotelling T2 statistic to compare the average shapes trends between two populations. We demonstrate the benefits of our method on a synthetic example of longitudinal tori and data from a developmental neuroimaging study.
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Muralidharan P, Fletcher PT. Sasaki Metrics for Analysis of Longitudinal Data on Manifolds. PROCEEDINGS. IEEE COMPUTER SOCIETY CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION 2012; 2012:1027-1034. [PMID: 25530694 DOI: 10.1109/cvpr.2012.6247780] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Longitudinal data arises in many applications in which the goal is to understand changes in individual entities over time. In this paper, we present a method for analyzing longitudinal data that take values in a Riemannian manifold. A driving application is to characterize anatomical shape changes and to distinguish between trends in anatomy that are healthy versus those that are due to disease. We present a generative hierarchical model in which each individual is modeled by a geodesic trend, which in turn is considered as a perturbation of the mean geodesic trend for the population. Each geodesic in the model can be uniquely parameterized by a starting point and velocity, i.e., a point in the tangent bundle. Comparison between these parameters is achieved through the Sasaki metric, which provides a natural distance metric on the tangent bundle. We develop a statistical hypothesis test for differences between two groups of longitudinal data by generalizing the Hotelling T 2 statistic to manifolds. We demonstrate the ability of these methods to distinguish differences in shape changes in a comparison of longitudinal corpus callosum data in subjects with dementia versus healthily aging controls.
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Sadeghi N, Prastawa M, Fletcher PT, Gilmore JH, Lin W, Gerig G. STATISTICAL GROWTH MODELING OF LONGITUDINAL DT-MRI FOR REGIONAL CHARACTERIZATION OF EARLY BRAIN DEVELOPMENT. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2012:1507-1510. [PMID: 23999084 DOI: 10.1109/isbi.2012.6235858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A population growth model that represents the growth trajectories of individual subjects is critical to study and understand neurodevelopment. This paper presents a framework for jointly estimating and modeling individual and population growth trajectories, and determining significant regional differences in growth pattern characteristics applied to longitudinal neuroimaging data. We use non-linear mixed effect modeling where temporal change is modeled by the Gompertz function. The Gompertz function uses intuitive parameters related to delay, rate of change, and expected asymptotic value; all descriptive measures which can answer clinical questions related to growth. Our proposed framework combines nonlinear modeling of individual trajectories, population analysis, and testing for regional differences. We apply this framework to the study of early maturation in white matter regions as measured with diffusion tensor imaging (DTI). Regional differences between anatomical regions of interest that are known to mature differently are analyzed and quantified. Experiments with image data from a large ongoing clinical study show that our framework provides descriptive, quantitative information on growth trajectories that can be directly interpreted by clinicians. To our knowledge, this is the first longitudinal analysis of growth functions to explain the trajectory of early brain maturation as it is represented in DTI.
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Singh N, Wang AY, Sankaranarayanan P, Fletcher PT, Joshi S. Genetic, structural and functional imaging biomarkers for early detection of conversion from MCI to AD. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2012; 15:132-40. [PMID: 23285544 DOI: 10.1007/978-3-642-33415-3_17] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
With the advent of advanced imaging techniques, genotyping, and methods to assess clinical and biological progression, there is a growing need for a unified framework that could exploit information available from multiple sources to aid diagnosis and the identification of early signs of Alzheimer's disease (AD). We propose a modeling strategy using supervised feature extraction to optimally combine high-dimensional imaging modalities with several other low-dimensional disease risk factors. The motivation is to discover new imaging biomarkers and use them in conjunction with other known biomarkers for prognosis of individuals at high risk of developing AD. Our framework also has the ability to assess the relative importance of imaging modalities for predicting AD conversion. We evaluate the proposed methodology on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database to predict conversion of individuals with mild cognitive impairment (MCI) to AD, only using information available at baseline.
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Anderson JS, Nielsen JA, Froehlich AL, DuBray MB, Druzgal TJ, Cariello AN, Cooperrider JR, Zielinski BA, Ravichandran C, Fletcher PT, Alexander AL, Bigler ED, Lange N, Lainhart JE. Functional connectivity magnetic resonance imaging classification of autism. ACTA ACUST UNITED AC 2011; 134:3742-54. [PMID: 22006979 DOI: 10.1093/brain/awr263] [Citation(s) in RCA: 276] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Group differences in resting state functional magnetic resonance imaging connectivity between individuals with autism and typically developing controls have been widely replicated for a small number of discrete brain regions, yet the whole-brain distribution of connectivity abnormalities in autism is not well characterized. It is also unclear whether functional connectivity is sufficiently robust to be used as a diagnostic or prognostic metric in individual patients with autism. We obtained pairwise functional connectivity measurements from a lattice of 7266 regions of interest covering the entire grey matter (26.4 million connections) in a well-characterized set of 40 male adolescents and young adults with autism and 40 age-, sex- and IQ-matched typically developing subjects. A single resting state blood oxygen level-dependent scan of 8 min was used for the classification in each subject. A leave-one-out classifier successfully distinguished autism from control subjects with 83% sensitivity and 75% specificity for a total accuracy of 79% (P = 1.1 × 10(-7)). In subjects <20 years of age, the classifier performed at 89% accuracy (P = 5.4 × 10(-7)). In a replication dataset consisting of 21 individuals from six families with both affected and unaffected siblings, the classifier performed at 71% accuracy (91% accuracy for subjects <20 years of age). Classification scores in subjects with autism were significantly correlated with the Social Responsiveness Scale (P = 0.05), verbal IQ (P = 0.02) and the Autism Diagnostic Observation Schedule-Generic's combined social and communication subscores (P = 0.05). An analysis of informative connections demonstrated that region of interest pairs with strongest correlation values were most abnormal in autism. Negatively correlated region of interest pairs showed higher correlation in autism (less anticorrelation), possibly representing weaker inhibitory connections, particularly for long connections (Euclidean distance >10 cm). Brain regions showing greatest differences included regions of the default mode network, superior parietal lobule, fusiform gyrus and anterior insula. Overall, classification accuracy was better for younger subjects, with differences between autism and control subjects diminishing after 19 years of age. Classification scores of unaffected siblings of individuals with autism were more similar to those of the control subjects than to those of the subjects with autism. These findings indicate feasibility of a functional connectivity magnetic resonance imaging diagnostic assay for autism.
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Hao X, Whitaker RT, Fletcher PT. Adaptive Riemannian metrics for improved geodesic tracking of white matter. INFORMATION PROCESSING IN MEDICAL IMAGING : PROCEEDINGS OF THE ... CONFERENCE 2011; 22:13-24. [PMID: 21761642 DOI: 10.1007/978-3-642-22092-0_2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We present a new geodesic approach for studying white matter connectivity from diffusion tensor imaging (DTI). Previous approaches have used the inverse diffusion tensor field as a Riemannian metric and constructed white matter tracts as geodesics on the resulting manifold. These geodesics have the desirable property that they tend to follow the main eigenvectors of the tensors, yet still have the flexibility to deviate from these directions when it results in lower costs. While this makes such methods more robust to noise, it also has the serious drawback that geodesics tend to deviate from the major eigenvectors in high-curvature areas in order to achieve the shortest path. In this paper we formulate a modification of the Riemannian metric that results in geodesics adapted to follow the principal eigendirection of the tensor even in high-curvature regions. We show that this correction can be formulated as a simple scalar field modulation of the metric and that the appropriate variational problem results in a Poisson's equation on the Riemannian manifold. We demonstrate that the proposed method results in improved geodesics using both synthetic and real DTI data.
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Lange N, Dubray MB, Lee JE, Froimowitz MP, Froehlich A, Adluru N, Wright B, Ravichandran C, Fletcher PT, Bigler ED, Alexander AL, Lainhart JE. Atypical diffusion tensor hemispheric asymmetry in autism. Autism Res 2010; 3:350-8. [PMID: 21182212 PMCID: PMC3215255 DOI: 10.1002/aur.162] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/21/2010] [Indexed: 11/12/2022]
Abstract
BACKGROUND Biological measurements that distinguish individuals with autism from typically developing individuals and those with other developmental and neuropsychiatric disorders must demonstrate very high performance to have clinical value as potential imaging biomarkers. We hypothesized that further study of white matter microstructure (WMM) in the superior temporal gyrus (STG) and temporal stem (TS), two brain regions in the temporal lobe containing circuitry central to language, emotion, and social cognition, would identify a useful combination of classification features and further understand autism neuropathology. METHODS WMM measurements from the STG and TS were examined from 30 high-functioning males satisfying full criteria for idiopathic autism aged 7-28 years and 30 matched controls and a replication sample of 12 males with idiopathic autism and 7 matched controls who participated in a previous case-control diffusion tensor imaging (DTI) study. Language functioning, adaptive functioning, and psychotropic medication usage were also examined. RESULTS In the STG, we find reversed hemispheric asymmetry of two separable measures of directional diffusion coherence, tensor skewness, and fractional anisotropy. In autism, tensor skewness is greater on the right and fractional anisotropy is decreased on the left. We also find increased diffusion parallel to white matter fibers bilaterally. In the right not left TS, we find increased omnidirectional, parallel, and perpendicular diffusion. These six multivariate measurements possess very high ability to discriminate individuals with autism from individuals without autism with 94% sensitivity, 90% specificity, and 92% accuracy in our original and replication samples. We also report a near-significant association between the classifier and a quantitative trait index of autism and significant correlations between two classifier components and measures of language, IQ, and adaptive functioning in autism.
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Singh N, Fletcher PT, Preston JS, Ha L, King R, Marron JS, Wiener M, Joshi S. Multivariate statistical analysis of deformation momenta relating anatomical shape to neuropsychological measures. ACTA ACUST UNITED AC 2010; 13:529-37. [PMID: 20879441 DOI: 10.1007/978-3-642-15711-0_66] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The purpose of this study is to characterize the neuroanatomical variations observed in neurological disorders such as dementia. We do a global statistical analysis of brain anatomy and identify the relevant shape deformation patterns that explain corresponding variations in clinical neuropsychological measures. The motivation is to model the inherent relation between anatomical shape and clinical measures and evaluate its statistical significance. We use Partial Least Squares for the multivariate statistical analysis of the deformation momenta under the Large Deformation Diffeomorphic framework. The statistical methodology extracts pertinent directions in the momenta space and the clinical response space in terms of latent variables. We report the results of this analysis on 313 subjects from the Mild Cognitive Impairment group in the Alzheimer's Disease Neuroimaging Initiative (ADNI).
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Fletcher PT, Kumar A, Wang AY, Jagust WJ, Chen K, Reiman EM, Weiner MW, Foster NL. IC‐P‐016: Regression‐to‐pons normalization of FDG‐PET improves discrimination of Alzheimer's disease from healthy aging. Alzheimers Dement 2010. [DOI: 10.1016/j.jalz.2010.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Foster NL, Wang AY, Fletcher PT, Joshi S, Minoshima S, Jagust WJ, Chen K, Reiman EM, Weiner MW. P1‐421: Topographic extent of cerebral hypometabolism predicts time of conversion from aMCI to Alzheimer's disease: Data from the Alzheimer's Disease Neuroimaging Initiative. Alzheimers Dement 2010. [DOI: 10.1016/j.jalz.2010.05.976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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