Diagnosis of autism spectrum disorders using regional and interregional morphological features

Denoising Diffusion-Weighted Images Using Grouped Iterative Hard Thresholding of Multi-Channel Framelets

Noise in diffusion-weighted (DW) images increases the complexity of quantitative analysis and decreases the reliability of inferences. Hence, to improve analysis, it is often desirable to remove noise and at the same time preserve relevant image features. In this paper, we propose a tight wavelet frame based approach for edge-preserving denoising of DW images. Our approach (i) employs the unitary extension principle (UEP) to generate frames that are discrete analogues to differential operators of various orders; (ii) introduces a very efficient method for solving an ℓ₀ denoising problem that involves only thresholding and solving a trivial inverse problem; and (iii) groups DW images acquired with neighboring gradient directions for collaborative denoising. Experiments using synthetic data with noncentral chi noise and real data with repeated scans confirm that our method yields superior performance compared with denoising using state-of-the-art methods such as non-local means.

Multi-modal, Multi-measure, and Multi-class Discrimination of ADHD with Hierarchical Feature Extraction and Extreme Learning Machine Using Structural and Functional Brain MRI

Structural and functional MRI unveil many hidden properties of the human brain. We performed this multi-class classification study on selected subjects from the publically available attention deficit hyperactivity disorder ADHD-200 dataset of patients and healthy children. The dataset has three groups, namely, ADHD inattentive, ADHD combined, and typically developing. We calculated the global averaged functional connectivity maps across the whole cortex to extract anatomical atlas parcellation based features from the resting-state fMRI (rs-fMRI) data and cortical parcellation based features from the structural MRI (sMRI) data. In addition, the preprocessed image volumes from both of these modalities followed an ANOVA analysis separately using all the voxels. This study utilized the average measure from the most significant regions acquired from ANOVA as features for classification in addition to the multi-modal and multi-measure features of structural and functional MRI data. We extracted most discriminative features by hierarchical sparse feature elimination and selection algorithm. These features include cortical thickness, image intensity, volume, cortical thickness standard deviation, surface area, and ANOVA based features respectively. An extreme learning machine performed both the binary and multi-class classifications in comparison with support vector machines. This article reports prediction accuracy of both unimodal and multi-modal features from test data. We achieved 76.190% (p < 0.0001) classification accuracy in multi-class settings as well as 92.857% (p < 0.0001) classification accuracy in binary settings. In addition, we found ANOVA-based significant regions of the brain that also play a vital role in the classification of ADHD. Thus, from a clinical perspective, this multi-modal group analysis approach with multi-measure features may improve the accuracy of the ADHD differential diagnosis.

Single subject prediction of brain disorders in neuroimaging: Promises and pitfalls

Neuroimaging-based single subject prediction of brain disorders has gained increasing attention in recent years. Using a variety of neuroimaging modalities such as structural, functional and diffusion MRI, along with machine learning techniques, hundreds of studies have been carried out for accurate classification of patients with heterogeneous mental and neurodegenerative disorders such as schizophrenia and Alzheimer's disease. More than 500 studies have been published during the past quarter century on single subject prediction focused on a multiple brain disorders. In the first part of this study, we provide a survey of more than 200 reports in this field with a focus on schizophrenia, mild cognitive impairment (MCI), Alzheimer's disease (AD), depressive disorders, autism spectrum disease (ASD) and attention-deficit hyperactivity disorder (ADHD). Detailed information about those studies such as sample size, type and number of extracted features and reported accuracy are summarized and discussed. To our knowledge, this is by far the most comprehensive review of neuroimaging-based single subject prediction of brain disorders. In the second part, we present our opinion on major pitfalls of those studies from a machine learning point of view. Common biases are discussed and suggestions are provided. Moreover, emerging trends such as decentralized data sharing, multimodal brain imaging, differential diagnosis, disease subtype classification and deep learning are also discussed. Based on this survey, there is extensive evidence showing the great potential of neuroimaging data for single subject prediction of various disorders. However, the main bottleneck of this exciting field is still the limited sample size, which could be potentially addressed by modern data sharing models such as the ones discussed in this paper. Emerging big data technologies and advanced data-intensive machine learning methodologies such as deep learning have coincided with an increasing need for accurate, robust and generalizable single subject prediction of brain disorders during an exciting time. In this report, we survey the past and offer some opinions regarding the road ahead.

Multivariate characterization of white matter heterogeneity in autism spectrum disorder

The complexity and heterogeneity of neuroimaging findings in individuals with autism spectrum disorder has suggested that many of the underlying alterations are subtle and involve many brain regions and networks. The ability to account for multivariate brain features and identify neuroimaging measures that can be used to characterize individual variation have thus become increasingly important for interpreting and understanding the neurobiological mechanisms of autism. In the present study, we utilize the Mahalanobis distance, a multidimensional counterpart of the Euclidean distance, as an informative index to characterize individual brain variation and deviation in autism. Longitudinal diffusion tensor imaging data from 149 participants (92 diagnosed with autism spectrum disorder and 57 typically developing controls) between 3.1 and 36.83 years of age were acquired over a roughly 10-year period and used to construct the Mahalanobis distance from regional measures of white matter microstructure. Mahalanobis distances were significantly greater and more variable in the autistic individuals as compared to control participants, demonstrating increased atypicalities and variation in the group of individuals diagnosed with autism spectrum disorder. Distributions of multivariate measures were also found to provide greater discrimination and more sensitive delineation between autistic and typically developing individuals than conventional univariate measures, while also being significantly associated with observed traits of the autism group. These results help substantiate autism as a truly heterogeneous neurodevelopmental disorder, while also suggesting that collectively considering neuroimaging measures from multiple brain regions provides improved insight into the diversity of brain measures in autism that is not observed when considering the same regions separately. Distinguishing multidimensional brain relationships may thus be informative for identifying neuroimaging-based phenotypes, as well as help elucidate underlying neural mechanisms of brain variation in autism spectrum disorders.

Anomalous gray matter patterns in specific reading comprehension deficit are independent of dyslexia

Specific reading comprehension deficit (SRCD) affects up to 10 % of all children. SRCD is distinct from dyslexia (DYS) in that individuals with SRCD show poor comprehension despite adequate decoding skills. Despite its prevalence and considerable behavioral research, there is not yet a unified cognitive profile of SRCD. While its neuroanatomical basis is unknown, SRCD could be anomalous in regions subserving their commonly reported cognitive weaknesses in semantic processing or executive function. Here we investigated, for the first time, patterns of gray matter volume difference in SRCD as compared to DYS and typical developing (TD) adolescent readers (N = 41). A linear support vector machine algorithm was applied to whole brain gray matter volumes generated through voxel-based morphometry. As expected, DYS differed significantly from TD in a pattern that included features from left fusiform and supramarginal gyri (DYS vs. TD: 80.0 %, p < 0.01). SRCD was well differentiated not only from TD (92.5 %, p < 0.001) but also from DYS (88.0 %, p < 0.001). Of particular interest were findings of reduced gray matter volume in right frontal areas that were also supported by univariate analysis. These areas are thought to subserve executive processes relevant for reading, such as monitoring and manipulating mental representations. Thus, preliminary analyses suggest that SRCD readers possess a distinct neural profile compared to both TD and DYS readers and that these differences might be linked to domain-general abilities. This work provides a foundation for further investigation into variants of reading disability beyond DYS.

Multi-Tissue Decomposition of Diffusion MRI Signals via Sparse-Group Estimation

Sparse estimation techniques are widely utilized in diffusion magnetic resonance imaging (DMRI). In this paper, we present an algorithm for solving the ℓ₀ sparse-group estimation problem and apply it to the tissue signal separation problem in DMRI. Our algorithm solves the ℓ₀ problem directly, unlike existing approaches that often seek to solve its relaxed approximations. We include the mathematical proofs showing that the algorithm will converge to a solution satisfying the firstorder optimality condition within a finite number of iterations. We apply this algorithm to DMRI data to tease apart signal contributions from white matter, gray matter, and cerebrospinal fluid with the aim of improving the estimation of the fiber orientation distribution function (FODF). Unlike spherical deconvolution approaches that assume an invariant fiber response function (RF), our approach utilizes an RF group to span the signal subspace of each tissue type, allowing greater flexibility in accounting for possible variations of the RF throughout space and within each voxel. Our ℓ₀ algorithm allows for the natural groupings of the RFs to be considered during signal decomposition. Experimental results confirm that our method yields estimates of FODFs and volume fractions of tissue compartments with improved robustness and accuracy. Our ℓ₀ algorithm is general and can be applied to sparse estimation problems beyond the scope of this paper.

The neuroanatomy of autism spectrum disorder: An overview of structural neuroimaging findings and their translatability to the clinical setting

Autism spectrum disorder is a complex neurodevelopmental disorder, which is accompanied by differences in brain anatomy, functioning and brain connectivity. Due to its neurodevelopmental character, and the large phenotypic heterogeneity among individuals on the autism spectrum, the neurobiology of autism spectrum disorder is inherently difficult to describe. Nevertheless, significant progress has been made in characterizing the neuroanatomical underpinnings of autism spectrum disorder across the human life span, and in identifying the molecular pathways that may be affected in autism spectrum disorder. Moreover, novel methodological frameworks for analyzing neuroimaging data are emerging that make it possible to characterize the neuroanatomy of autism spectrum disorder on the case level, and to stratify individuals based on their individual phenotypic make up. While these approaches are increasingly more often employed in the research setting, their applicability in the clinical setting remains a vision for the future. The aim of the current review is to (1) provide a general overview of recent structural neuroimaging findings examining the neuroanatomy of autism spectrum disorder across the human life span, and in males and females with the condition, (2) highlight potential neuroimaging (bio)markers that may in the future be used for the stratification of autism spectrum disorder individuals into biologically homogeneous subgroups and (3) inform treatment and intervention strategies.

One-Class Support Vector Machines Identify the Language and Default Mode Regions As Common Patterns of Structural Alterations in Young Children with Autism Spectrum Disorders

The identification of reliable brain endophenotypes of autism spectrum disorders (ASD) has been hampered to date by the heterogeneity in the neuroanatomical abnormalities detected in this condition. To handle the complexity of neuroimaging data and to convert brain images in informative biomarkers of pathology, multivariate analysis techniques based on Support Vector Machines (SVM) have been widely used in several disease conditions. They are usually trained to distinguish patients from healthy control subjects by making a binary classification. Here, we propose the use of the One-Class Classification (OCC) or Data Description method that, in contrast to two-class classification, is based on a description of one class of objects only. This approach, by defining a multivariate normative rule on one class of subjects, allows recognizing examples from a different category as outliers. We applied the OCC to 314 regional features extracted from brain structural Magnetic Resonance Imaging (MRI) scans of young children with ASD (21 males and 20 females) and control subjects (20 males and 20 females), matched on age [range: 22-72 months of age; mean = 49 months] and non-verbal intelligence quotient (NVIQ) [range: 31-123; mean = 73]. We demonstrated that a common pattern of features characterize the ASD population. The OCC SVM trained on the group of ASD subjects showed the following performances in the ASD vs. controls separation: the area under the receiver operating characteristic curve (AUC) was 0.74 for the male and 0.68 for the female population, respectively. Notably, the ASD vs. controls discrimination results were maximized when evaluated on the subsamples of subjects with NVIQ ≥ 70, leading to AUC = 0.81 for the male and AUC = 0.72 for the female populations, respectively. Language regions and regions from the default mode network-posterior cingulate cortex, pars opercularis and pars triangularis of the inferior frontal gyrus, and transverse temporal gyrus-contributed most to distinguishing individuals with ASD from controls, arguing for the crucial role of these areas in the ASD pathophysiology. The observed brain patterns associate preschoolers with ASD independently of their age, gender and NVIQ and therefore they are expected to constitute part of the ASD brain endophenotype.

Divide and Conquer: Sub-Grouping of ASD Improves ASD Detection Based on Brain Morphometry

Low success (<60%) in autism spectrum disorder (ASD) classification using brain morphometry from the large multi-site ABIDE dataset and inconsistent findings on brain morphometric abnormalities in ASD can be attributed to the ASD heterogeneity. In this study, we show that ASD brain morphometry is highly heterogeneous, and demonstrate that the heterogeneity can be mitigated and classification improved if autism severity (AS), verbal IQ (VIQ) and age are used with morphometric features. Morphometric features from structural MRIs (sMRIs) of 734 males (ASD: 361, controls: 373) of ABIDE were derived using FreeSurfer. Applying the Random Forest classifier, an AUC of 0.61 was achieved. Adding VIQ and age to morphometric features, AUC improved to 0.68. Sub-grouping the subjects by AS, VIQ and age improved the classification with the highest AUC of 0.8 in the moderate-AS sub-group (AS = 7–8). Matching subjects on age and/or VIQ in each sub-group further improved the classification with the highest AUC of 0.92 in the low AS sub-group (AS = 4–5). AUC decreased with AS and VIQ, and was the lowest in the mid-age sub-group (13–18 years). The important features were mainly from the frontal, temporal, ventricular, right hippocampal and left amygdala regions. However, they highly varied with AS, VIQ and age. The curvature and folding index features from frontal, temporal, lingual and insular regions were dominant in younger subjects suggesting their importance for early detection. When the experiments were repeated using the Gradient Boosting classifier similar results were obtained. Our findings suggest that identifying brain biomarkers in sub-groups of ASD can yield more robust and insightful results than searching across the whole spectrum. Further, it may allow identification of sub-group specific brain biomarkers that are optimized for early detection and monitoring, increasing the utility of sMRI as an important tool for early detection of ASD.

Multi-task feature selection via supervised canonical graph matching for diagnosis of autism spectrum disorder

In this paper, we propose a novel framework for ASD diagnosis using structural magnetic resonance imaging (MRI). Our method deals explicitly with the distributional differences of gray matter (GM) and white matter (WM) features extracted from MR images. We project linearly the GM and WM features onto a canonical space where their correlations are mutually maximized. In this canonical space, features that are highly correlated with the class labels are selected for ASD diagnosis. In addition, graph matching is employed to preserve the geometrical relationships between samples when projected onto the canonical space. Our evaluations based on a public ASD dataset show that the proposed method outperforms all competing methods on all clinically important measures in differentiating ASD patients from healthy individuals.

Diagnosis of Autism Spectrum Disorders Using Temporally Distinct Resting-State Functional Connectivity Networks

INTRODUCTION

Resting-state functional magnetic resonance imaging (R-fMRI) is dynamic in nature as neural activities constantly change over the time and are dominated by repeating brief activations and deactivations involving many brain regions. Each region participates in multiple brain functions and is part of various functionally distinct but spatially overlapping networks. Functional connectivity computed as correlations over the entire time series always overlooks interregion interactions that often occur repeatedly and dynamically in time, limiting its application to disease diagnosis.

AIMS

We develop a novel framework that uses short-time activation patterns of brain connectivity to better detect subtle disease-induced disruptions of brain connectivity. A clustering algorithm is first used to temporally decompose R-fMRI time series into distinct clusters with similar spatial distribution of neural activity based on the assumption that functionally distinct networks should be largely temporally distinct as brain states do not simultaneously coexist in general. A Pearson correlation-based functional connectivity network is then constructed for each cluster to allow for better exploration of spatiotemporal dynamics of individual neural activity. To reduce significant intersubject variability and to remove possible spurious connections, we use a group-constrained sparse regression model to construct a backbone sparse network for each cluster and use it to weight the corresponding Pearson correlation network.

RESULTS

The proposed method outperforms the conventional static, temporally dependent fully connected correlation-based networks by at least 7% on a publicly available autism dataset. We were able to reproduce similar results using data from other centers.

CONCLUSIONS

By combining the advantages of temporal independence and group-constrained sparse regression, our method improves autism diagnosis.

Multivariate analyses applied to fetal, neonatal and pediatric MRI of neurodevelopmental disorders

Multivariate analysis (MVA) is a class of statistical and pattern recognition methods that involve the processing of data that contains multiple measurements per sample. MVA can be used to address a wide variety of medical neuroimaging-related challenges including identifying variables associated with a measure of clinical importance (i.e. patient outcome), creating diagnostic tests, assisting in characterizing developmental disorders, understanding disease etiology, development and progression, assisting in treatment monitoring and much more. Compared to adults, imaging of developing immature brains has attracted less attention from MVA researchers. However, remarkable MVA research growth has occurred in recent years. This paper presents the results of a systematic review of the literature focusing on MVA technologies applied to neurodevelopmental disorders in fetal, neonatal and pediatric magnetic resonance imaging (MRI) of the brain. The goal of this manuscript is to provide a concise review of the state of the scientific literature on studies employing brain MRI and MVA in a pre-adult population. Neurological developmental disorders addressed in the MVA research contained in this review include autism spectrum disorder, attention deficit hyperactivity disorder, epilepsy, schizophrenia and more. While the results of this review demonstrate considerable interest from the scientific community in applications of MVA technologies in pediatric/neonatal/fetal brain MRI, the field is still young and considerable research growth remains ahead of us.

Identification of Infants at Risk for Autism Using Multi-parameter Hierarchical White Matter Connectomes

Autism spectrum disorder (ASD) is a variety of developmental disorders that cause life-long communication and social deficits. However, ASD could only be diagnosed at children as early as 2 years of age, while early signs may emerge within the first year. White matter (WM) connectivity abnormalities have been documented in the first year of lives of ASD subjects. We introduce a novel multi-kernel support vector machine (SVM) framework to identify infants at high-risk for ASD at 6 months old, by utilizing the diffusion parameters derived from a hierarchical set of WM connectomes. Experiments show that the proposed method achieves an accuracy of 76%, in comparison to 70% with the best single connectome. The complementary information extracted from hierarchical networks enhances the classification performance, with the top discriminative connections consistent with other studies. Our framework provides essential imaging connectomic markers and contributes to the evaluation of ASD risks as early as 6 months.

Identification of infants at high-risk for autism spectrum disorder using multiparameter multiscale white matter connectivity networks

Autism spectrum disorder (ASD) is a wide range of disabilities that cause life-long cognitive impairment and social, communication, and behavioral challenges. Early diagnosis and medical intervention are important for improving the life quality of autistic patients. However, in the current practice, diagnosis often has to be delayed until the behavioral symptoms become evident during childhood. In this study, we demonstrate the feasibility of using machine learning techniques for identifying high-risk ASD infants at as early as six months after birth. This is based on the observation that ASD-induced abnormalities in white matter (WM) tracts and whole-brain connectivity have already started to appear within 24 months after birth. In particular, we propose a novel multikernel support vector machine classification framework by using the connectivity features gathered from WM connectivity networks, which are generated via multiscale regions of interest (ROIs) and multiple diffusion statistics such as fractional anisotropy, mean diffusivity, and average fiber length. Our proposed framework achieves an accuracy of 76% and an area of 0.80 under the receiver operating characteristic curve (AUC), in comparison to the accuracy of 70% and the AUC of 70% provided by the best single-parameter single-scale network. The improvement in accuracy is mainly due to the complementary information provided by multiparameter multiscale networks. In addition, our framework also provides the potential imaging connectomic markers and an objective means for early ASD diagnosis.

From estimating activation locality to predicting disorder: A review of pattern recognition for neuroimaging-based psychiatric diagnostics

Psychiatric disorders are increasingly being recognised as having a biological basis, but their diagnosis is made exclusively behaviourally. A promising approach for 'biomarker' discovery has been based on pattern recognition methods applied to neuroimaging data, which could yield clinical utility in future. In this review we survey the literature on pattern recognition for making diagnostic predictions in psychiatric disorders, and evaluate progress made in translating such findings towards clinical application. We evaluate studies on many criteria, including data modalities used, the types of features extracted and algorithm applied. We identify problems common to many studies, such as a relatively small sample size and a primary focus on estimating generalisability within a single study. Furthermore, we highlight challenges that are not widely acknowledged in the field including the importance of accommodating disease prevalence, the necessity of more extensive validation using large carefully acquired samples, the need for methodological innovations to improve accuracy and to discriminate between multiple disorders simultaneously. Finally, we identify specific clinical contexts in which pattern recognition can add value in the short to medium term.

Neuroimaging in autism spectrum disorder: brain structure and function across the lifespan

Over the past decade, in-vivo MRI studies have provided many invaluable insights into the neural substrates underlying autism spectrum disorder (ASD), which is now known to be associated with neurodevelopmental variations in brain anatomy, functioning, and connectivity. These systems-level features of ASD pathology seem to develop differentially across the human lifespan so that the cortical abnormalities that occur in children with ASD differ from those noted at other stages of life. Thus, investigation of the brain in ASD poses particular methodological challenges, which must be addressed to enable the comparison of results across studies. Novel analytical approaches are also being developed to facilitate the translation of findings from the research to the clinical setting. In the future, the insights provided by human neuroimaging studies could contribute to biomarker development for ASD and other neurodevelopmental disorders, and to new approaches to diagnosis and treatment.