The white matter connectome as an individualized biomarker of language impairment in temporal lobe epilepsy.

ObjectiveThe distributed white matter network underlying language leads to difficulties in extracting clinically meaningful summaries of neural alterations leading to language impairment. Here we determine the predictive ability of the structural connectome (SC), compared with global measures of white matter tract microstructure and clinical data, to discriminate language impaired patients with temporal lobe epilepsy (TLE) from TLE patients without language impairment.MethodsT1- and diffusion-MRI, clinical variables (CVs), and neuropsychological measures of naming and verbal fluency were available for 82 TLE patients. Prediction of language impairment was performed using a robust tree-based classifier (XGBoost) for three models: (1) a CV-model which included demographic and epilepsy-related clinical features, (2) an atlas-based tract-model, including four frontotemporal white matter association tracts implicated in language (i.e., the bilateral arcuate fasciculus, inferior frontal occipital fasciculus, inferior longitudinal fasciculus, and uncinate fasciculus), and (3) a SC-model based on diffusion MRI. For the association tracts, mean fractional anisotropy was calculated as a measure of white matter microstructure for each tract using a diffusion tensor atlas (i.e., AtlasTrack). The SC-model used measurement of cortical-cortical connections arising from a temporal lobe subnetwork derived using probabilistic tractography. Dimensionality reduction of the SC was performed with principal components analysis (PCA). Each model was trained on 49 patients from one epilepsy center and tested on 33 patients from a different center (i.e., an independent dataset). Randomization was performed to test the stability of the results.ResultsThe SC-model yielded a greater area under the curve (AUC; .73) and accuracy (79%) compared to both the tract-model (AUC: .54, p < .001; accuracy: 70%, p < .001) and the CV-model (AUC: .59, p < .001; accuracy: 64%, p < .001). Within the SC-model, lateral temporal connections had the highest importance to model performance, including connections similar to language association tracts such as links between the superior temporal gyrus to pars opercularis. However, in addition to these connections many additional connections that were widely distributed, bilateral and interhemispheric in nature were identified as contributing to SC-model performance.ConclusionThe SC revealed a white matter network contributing to language impairment that was widely distributed, bilateral, and lateral temporal in nature. The distributed network underlying language may be why the SC-model has an advantage in identifying sub-components of the complex fiber networks most relevant for aspects of language performance

Physiological and pathological modulations of intrinsic brain activity assessed via resting-state fMRI

Since its inception in 1992, functional magnetic resonance imaging (fMRI) has considerably boosted our knowledge of the human brain function, primarily due to its non-invasive nature, and its relative high spatial and temporal resolution. Among the available fMRI contrasts, blood-oxygenation level-dependent (BOLD) signal plays a leading role in this field. The contrast is based on the different magnetic properties of the haemoglobin which - combined with the specific relation existing between neuronal, vascular and metabolic activity - allows to ascribe variations in the measured signal to variations in the underlying neuronal activity. During BOLD acquisitions, the comparison of different cognitive states in task-based experiment (alternating rest states to sensory or cognitive stimulations) has revealed the modular organization of the human brain function, an operation that is commonly referred to as functional brain mapping. Surprisingly, task-induced activity requires an increase in brain’s energy consumption by less than 5 percent of the underlying baseline activity. Most of the brain’s energy demand, from 60 to 80 percent, is used to sustain intrinsic, task-unrelated, neural activity (Raichle, 2006). In this light, functional brain mapping, utilizing task-based fMRI, focuses only on the tip of the iceberg, whereas most of the brain’s activity remains largely uncharted. The notion that the brain has an intrinsic or spontaneous activity is known from early electro-encephalography (EEG) measures due to Hans Berger. However, only in recent years, after the seminal work of Biswal and colleagues (Biswal et al., 1995), the study of spontaneous brain activity has overwhelmingly emerged as a primary field of research in neuroscience. In the so called resting-state condition (i.e., when the brain is not focused on the external world), Biswal reported BOLD low-frequency (< 0.1 Hz) fluctuations (LFFs) synchronized across functionally related and anatomically connected regions. Thereafter, several studies have consistently shown that specific patterns of synchronized spontaneous LFFs identify different resting-state networks, including, but not limited to, visual, motor, auditory, and attentive network. The overall picture emerging from thousands of resting-state fMRI studies depicts a never-resting brain, continuously engaged in maintaining communications within several wide-distributed networks. Such intrinsic brain activity, reflected in spontaneous BOLD LFFs, is the focus of the present thesis. The study of LFFs in spontaneous BOLD signal can reveal much about brain’s functional organization, especially considering that signal variability has been related to variability in behaviour (Fox et al., 2007). In addition, the simplicity of data acquisition – subjects just lie in the scanner refraining from falling asleep - makes the technique particularly suited for studying pathological conditions, in which subject’s cooperation might not fulfil the demands of task-based studies. Indeed, several psychiatric and neurological disorders, including degenerative dementia, have shown altered patterns of LFFs, even in the absence of observable anatomical abnormalities (Barkhof et al., 2014). Thus, how the intrinsic brain’s activity is modulated in response to different behavioural states and in response to pathological conditions can give insights into the brain functionality and into the mechanisms behind illnesses, respectively. Importantly, correct result interpretation is highly influenced by the type of metrics adopted and how they are implemented. The resting-state approach to the study of the brain’s function has required the development of more sophisticated processing and analysis techniques compared to those commonly applied in task-based fMRI. While seeking for task-responding regions in the brain is guided by information embedded in the experimental paradigm, in steady-state fMRI no a priori cue is provided. In such experiment the extraction of relevant information is based on (i) the temporal synchronization between spatially segregated elements of the brain, feature known as functional connectivity, and on (ii) the amplitude of the oscillation per se, a measure of the strength of the intrinsic brain activity. Despite such simple classification, the field of resting-state fMRI is scattered with a disparate amount of metrics, each of which highlight different facets of spontaneous LFFs. Before turning to the study of spontaneous LFF modulations, we will provide a comprehensive and optimized mathematical framework for the extraction of relevant information from resting-state data (Chapter 2). The results of this effort is an easy-to-use matlab toolbox specifically designed for the processing and analysis of steady-state fMRI data. In principle, the information coded in functional connectivity and in oscillation amplitude are unrelated. While the former assesses the degree of cooperation between segregated elements of the brain, the latter quantifies the neural workload of each single brain’s element, independently from the activity of other regions. Nonetheless, modulations in both measurements have been reported in several pathological conditions - yet in separate studies - suggesting a possible relation between them. In this context, we sought to investigate the potential coupling between the functional connectivity and the oscillation amplitude in cohort of healthy elderly and the probable modulations induced by dementia of the Alzheimer’s type (Chapter 3). Regardless of how the brain relates the two types of measures extractable from resting-state data, their disease-induced modulations are relevant per se in uncovering the illness. Indeed, Alzheimer’s disease is known to produce alterations in spontaneous brain activity, both at the synchronization and the amplitude level (Wang et al., 2007). Since the hallmark of the pathology is a profound deficit in episodic memory, much effort has been done in characterizing the alterations in spontaneous brain activity underlying such deficit. Contrarily, little is known about another commonly reported deficit, the language related impairment (Taler and Phillips, 2008). In the second part of Chapter 3 we sought to disclose the brain regions underpinning language deficits by looking at the alterations in functional connectivity of the relevant network. While the study of LFFs in pathological conditions can contribute to reveal the mechanisms behind the pathology and how it spreads into the brain, the study of spontaneous brain activity in physiological conditions can disclose the intrinsic brain functionality. In healthy subjects the resting brain has been extensively characterized and its network topology has shown to be a consistent and reliable physiological feature (Damoiseaux et al., 2006). An intriguing issue is how the brain reorganizes its patterns of spontaneous BOLD LFF while it is focusing on the external world. Indeed, the intrinsic brain activity is not an exclusive feature of the resting condition, instead it is present also on the top of the task-evoked response. In chapter 4, with peculiar experimental paradigms we separated the task-evoked response from the intrinsic brain activity during sustained cognitive stimulations. In a first experiment we sought to characterize the spatio-temporal proprieties and the dynamic of the transition from a resting to a stimulated condition. In the second part we specifically investigated how the brain reorganizes its internal functional architecture during visuospatial attention. Indeed, besides strongly affecting the processing of visual incoming stimuli, visual spatial attention also affects brain networks. Recent studies suggest that visual attention affects functional connectivity within and between the visual network and the attention network (Spadone et al., 2015), yet modulations of attention on brain networks are still poorly understood

Using brain connectomics to detect functional connectivity differences in Alzheimer's disease

Indiana University-Purdue University Indianapolis (IUPUI)Prodromal Alzheimer’s disease (AD) has recently been identified as a disease state where pathophysiological changes may progress despite the absence of significant clinical symptoms. Yet, the specific processes of neural dysfunction occurring during this preclinical phase remain unclear. Resting state fMRI (RS-fMRI) in combination with brain connectomic measurements may be able to provide ways to measure subtle connectivity changes in different neurological disease states. For instance, RS-fMRI scans allow us to determine functionally connected yet spatially distinct brain regions that can then be separated into resting-state networks (RSNs). More recently, the exploration of RSNs in disease states have proved promising since they have been reliably altered when compared to a control population. By using brain connectomic approaches to assess functional connectivity we can evaluate the human connectome from a different and more global perspective to help us better understand and detect prodromal neurodegenerative disease states

Network-based atrophy modelling in the common epilepsies: a worldwide ENIGMA study

SUMMARY Epilepsy is increasingly conceptualized as a network disorder. In this cross-sectional mega-analysis, we integrated neuroimaging and connectome analysis to identify network associations with atrophy patterns in 1,021 adults with epilepsy compared to 1,564 healthy controls from 19 international sites. In temporal lobe epilepsy, areas of atrophy co-localized with highly interconnected cortical hub regions, whereas idiopathic generalized epilepsy showed preferential subcortical hub involvement. These morphological abnormalities were anchored to the connectivity profiles of distinct disease epicenters, pointing to temporo-limbic cortices in temporal lobe epilepsy and fronto-central cortices in idiopathic generalized epilepsy. Indices of progressive atrophy further revealed a strong influence of connectome architecture on disease progression in temporal lobe, but not idiopathic generalized, epilepsy. Our findings were reproduced across individual sites and single patients, and were robust across different analytical methods. Through worldwide collaboration in ENIGMA-Epilepsy, we provided novel insights into the macroscale features that shape the pathophysiology of common epilepsies

Computer aided diagnosis in temporal lobe epilepsy and Alzheimer's dementia

Computer aided diagnosis within neuroimaging must rely on advanced image processing techniques to detect and quantify subtle signal changes that may be surrogate indicators of disease state. This thesis proposes two such novel methodologies that are both based on large volumes of interest, are data driven, and use cross-sectional scans: appearance-based classification (ABC) and voxel-based classification (VBC).The concept of appearance in ABC represents the union of intensity and shape information extracted from magnetic resonance images (MRI). The classification method relies on a linear modeling of appearance features via principal components analysis, and comparison of the distribution of projection coordinates for the populations under study within a reference multidimensional appearance eigenspace. Classification is achieved using forward, stepwise linear discriminant analyses, in multiple cross-validated trials. In this work, the ABC methodology is shown to accurately lateralize the seizure focus in temporal lobe epilepsy (TLE), differentiate normal aging individuals from patients with either Alzheimer's dementia (AD) or Mild Cognitive Impairment (MCI), and finally predict the progression of MCI patients to AD. These applications demonstrated that the ABC technique is robust to different signal changes due to two distinct pathologies, to low resolution data and motion artifacts, and to possible differences inherent to multi-site acquisition.The VBC technique relies on voxel-based morphometry to identify regions of grey and white matter concentration differences between co-registered cohorts of individuals, and then on linear modeling of variables extracted from these regions. Classification is achieved using linear discriminant analyses within a multivariate space composed of voxel-based morphometry measures related to grey and white matter concentration, along with clinical variables of interest. VBC is shown to increase the accuracy of prediction of one-year clinical status from three to four out of five TLE patients having undergone selective amygdalo-hippocampectomy. These two techniques are shown to have the necessary potential to solve current problems in neurological research, assist clinical physicians with their decision-making process and influence positively patient management

Doctor of Philosophy

dissertationThe human brain is the seat of cognition and behavior. Understanding the brain mechanistically is essential for appreciating its linkages with cognitive processes and behavioral outcomes in humans. Mechanisms of brain function categorically represent rich and widely under-investigated biological substrates for neural-driven studies of psychiatry and mental health. Research examining intrinsic connectivity patterns across whole brain systems utilizes functional magnetic resonance imaging (fMRI) to trace spontaneous fluctuations in blood oxygen-level dependent (BOLD) signals. In the first study presented, we reveal patterns of dynamic attractors in resting state functional connectivity data corresponding to well-documented biological networks. We introduce a novel simulation for whole brain dynamics that can be adapted to either group-level analysis or single-subject level models. We describe stability of intrinsic functional architecture in terms of transient and global steady states resembling biological networks. In the second study, we demonstrate plasticity in functional connectivity following a minimum six-week intervention to train cognitive performance in a speed reading task. Long-term modulation of connectivity with language regions indicate functional connectivity as a candidate biomarker for tracking and measuring functional changes in neural systems as outcomes of cognitive training. The third study demonstrates utility of functional biomarkers in predicting individual differences in behavioral and cognitive features. We successfully predict three major domains of personality psychologyintelligence, agreeableness, and conscientiousnessin individual subjects using a large (N=475) open source data sample compiled by the National Institutes of Healths Human Connectome Project

정신증 초고위험군과 초발정신병에서 뇌 백질 네트워크의 차등적 변화

학위논문 (박사)-- 서울대학교 대학원 : 뇌인지과학과, 2015. 8. 권준수.A comprehensive figure of dysconnectivity in schizophrenia could be explored at the network level that not only accounts for local but also global organizational characteristics. However, no study has concurrently explored alteration in the white matter (WM) network of the brain of first-episode psychosis (FEP) and its prodromal stage to see whether differential changes in the structural network would exist according to the different stages of psychosis. Thirty-seven subjects with ultra-high risk for psychosis (UHR), 21 patients with FEP, and 37 healthy controls (HC) were recruited in the study. 3-Tesla T1 structural and diffusion tensor images were reconstructed as weighted WM networks of the brain by measuring number of axonal streamlines between 82 cortical and subcortical regions. Then, graph measures extracted from the networks were compared. Although global graph measures reflecting efficiency or small-world property of a network were not different between groups, the UHR group showed a higher assortativity coefficient compared to the FEP group and a higher modularity Q, without alteration in global clustering coefficient, compared to the HC group. At the local level, the FEP group showed a weaker WM connection between the left hippocampus and ipsilateral parahippocampal gyrus and a stronger WM connection between the left thalamus and ipsilateral superior frontal gyrus compared to the UHR and HC groups. More rightward asymmetry of the connections between both hippocampi and ipsilateral parahippocampal gyri was seen in the FEP compared to the UHR and HC groups, and rightward asymmetry of the connections correlated positively with psychotic symptoms and negatively with level of functioning in the UHR group. The participation coefficient of the right pallidum increased in the FEP compared to the UHR and HC groups, and the measure positively correlated with nonspecific psychiatric symptoms in the FEP group. UHR has enhanced resilience and adaptability of the WM network that may reflect highly variable prognosis of the stage among psychosis-continuum and defensive mechanism of the network against further damage. On the other hand, FEP has alteration mainly in the cortico-subcortical connectivity. These differential changes may reflect underlying biological mechanisms of developmental process leading to psychosis.Abstract ------------------------------------------------------------------------------ i Contents ---------------------------------------------------------------------------- iii List of Tables ---------------------------------------------------------------------- iv List of Figures ---------------------------------------------------------------------- v List of Abbreviations ------------------------------------------------------------- vi I. Introduction -------------------------------------------------------------------- 1 II. Methods ------------------------------------------------------------------------ 8 III. Results ------------------------------------------------------------------------ 24 IV. Discussion -------------------------------------------------------------------- 35 V. Conclusion -------------------------------------------------------------------- 45 VI. Reference -------------------------------------------------------------------- 46 VII. Appendix ------------------------------------------------------------------- 63 국문초록 ------------------------------------------------------------------------ 78Docto

Genetic architecture of the white matter connectome of the human brain

White matter tracts form the structural basis of large-scale functional networks in the human brain. We applied brain-wide tractography to diffusion images from 30,810 adult participants (UK Biobank), and found significant heritability for 90 regional connectivity measures and 851 tract-wise connectivity measures. Multivariate genome- wide association analyses identified 355 independently associated lead SNPs across the genome, of which 77% had not been previously associated with human brain metrics. Enrichment analyses implicated neurodevelopmental processes including neurogenesis, neural differentiation, neural migration, neural projection guidance, and axon development, as well as prenatal brain expression especially in stem cells, astrocytes, microglia and neurons. We used the multivariate association profiles of lead SNPs to identify 26 genomic loci implicated in structural connectivity between core regions of the left-hemisphere language network, and also identified 6 loci associated with hemispheric left-right asymmetry of structural connectivity. Polygenic scores for schizophrenia, bipolar disorder, autism spectrum disorder, attention-deficit hyperactivity disorder, left-handedness, Alzheimer’s disease, amyotrophic lateral sclerosis, and epilepsy showed significant multivariate associations with structural connectivity, each implicating distinct sets of brain regions with trait-relevant functional profiles. This large-scale mapping study revealed common genetic contributions to the structural connectome of the human brain in the general adult population, highlighting links with polygenic disposition to brain disorders and behavioural traits

Deep Interpretability Methods for Neuroimaging

Brain dynamics are highly complex and yet hold the key to understanding brain function and dysfunction. The dynamics captured by resting-state functional magnetic resonance imaging data are noisy, high-dimensional, and not readily interpretable. The typical approach of reducing this data to low-dimensional features and focusing on the most predictive features comes with strong assumptions and can miss essential aspects of the underlying dynamics. In contrast, introspection of discriminatively trained deep learning models may uncover disorder-relevant elements of the signal at the level of individual time points and spatial locations. Nevertheless, the difficulty of reliable training on high-dimensional but small-sample datasets and the unclear relevance of the resulting predictive markers prevent the widespread use of deep learning in functional neuroimaging. In this dissertation, we address these challenges by proposing a deep learning framework to learn from high-dimensional dynamical data while maintaining stable, ecologically valid interpretations. The developed model is pre-trainable and alleviates the need to collect an enormous amount of neuroimaging samples to achieve optimal training. We also provide a quantitative validation module, Retain and Retrain (RAR), that can objectively verify the higher predictability of the dynamics learned by the model. Results successfully demonstrate that the proposed framework enables learning the fMRI dynamics directly from small data and capturing compact, stable interpretations of features predictive of function and dysfunction. We also comprehensively reviewed deep interpretability literature in the neuroimaging domain. Our analysis reveals the ongoing trend of interpretability practices in neuroimaging studies and identifies the gaps that should be addressed for effective human-machine collaboration in this domain. This dissertation also proposed a post hoc interpretability method, Geometrically Guided Integrated Gradients (GGIG), that leverages geometric properties of the functional space as learned by a deep learning model. With extensive experiments and quantitative validation on MNIST and ImageNet datasets, we demonstrate that GGIG outperforms integrated gradients (IG), which is considered to be a popular interpretability method in the literature. As GGIG is able to identify the contours of the discriminative regions in the input space, GGIG may be useful in various medical imaging tasks where fine-grained localization as an explanation is beneficial