Functional connectivity in relation to motor performance and recovery after stroke.

Plasticity after stroke has traditionally been studied by observing changes only in the spatial distribution and laterality of focal brain activation during affected limb movement. However, neural reorganization is multifaceted and our understanding may be enhanced by examining dynamics of activity within large-scale networks involved in sensorimotor control of the limbs. Here, we review functional connectivity as a promising means of assessing the consequences of a stroke lesion on the transfer of activity within large-scale neural networks. We first provide a brief overview of techniques used to assess functional connectivity in subjects with stroke. Next, we review task-related and resting-state functional connectivity studies that demonstrate a lesion-induced disruption of neural networks, the relationship of the extent of this disruption with motor performance, and the potential for network reorganization in the presence of a stroke lesion. We conclude with suggestions for future research and theories that may enhance the interpretation of changing functional connectivity. Overall findings suggest that a network level assessment provides a useful framework to examine brain reorganization and to potentially better predict behavioral outcomes following stroke

A group model for stable multi-subject ICA on fMRI datasets

Spatial Independent Component Analysis (ICA) is an increasingly used data-driven method to analyze functional Magnetic Resonance Imaging (fMRI) data. To date, it has been used to extract sets of mutually correlated brain regions without prior information on the time course of these regions. Some of these sets of regions, interpreted as functional networks, have recently been used to provide markers of brain diseases and open the road to paradigm-free population comparisons. Such group studies raise the question of modeling subject variability within ICA: how can the patterns representative of a group be modeled and estimated via ICA for reliable inter-group comparisons? In this paper, we propose a hierarchical model for patterns in multi-subject fMRI datasets, akin to mixed-effect group models used in linear-model-based analysis. We introduce an estimation procedure, CanICA (Canonical ICA), based on i) probabilistic dimension reduction of the individual data, ii) canonical correlation analysis to identify a data subspace common to the group iii) ICA-based pattern extraction. In addition, we introduce a procedure based on cross-validation to quantify the stability of ICA patterns at the level of the group. We compare our method with state-of-the-art multi-subject fMRI ICA methods and show that the features extracted using our procedure are more reproducible at the group level on two datasets of 12 healthy controls: a resting-state and a functional localizer study

Pitfalls in fMRI

Several different techniques allow a functional assessment of neuronal activations by magnetic resonance imaging (fMRI). The by far most influential fMRI technique is based on a local T2*-sensitive hemodynamic response to neuronal activation, also known as the blood oxygenation level dependent or BOLD effect. Consequently, the term ‘fMRI' is often used synonymously with BOLD imaging. Because interpretations of fMRI brain activation maps often appear intuitive and compelling, the reader might be tempted not to critically question the fundamental processes and assumptions. We review some essential processes and assumptions of BOLD fMRI and discuss related confounds and pitfalls in fMRI - from the underlying physiological effect, to data acquisition, data analysis and the interpretation of the results including clinical fMRI. A background framework is provided for the systematic and critical interpretation of fMRI result

Generative-Discriminative Low Rank Decomposition for Medical Imaging Applications

In this thesis, we propose a method that can be used to extract biomarkers from medical images toward early diagnosis of abnormalities. Surge of demand for biomarkers and availability of medical images in the recent years call for accurate, repeatable, and interpretable approaches for extracting meaningful imaging features. However, extracting such information from medical images is a challenging task because the number of pixels (voxels) in a typical image is in order of millions while even a large sample-size in medical image dataset does not usually exceed a few hundred. Nevertheless, depending on the nature of an abnormality, only a parsimonious subset of voxels is typically relevant to the disease; therefore various notions of sparsity are exploited in this thesis to improve the generalization performance of the prediction task. We propose a novel discriminative dimensionality reduction method that yields good classification performance on various datasets without compromising the clinical interpretability of the results. This is achieved by combining the modelling strength of generative learning framework and the classification performance of discriminative learning paradigm. Clinical interpretability can be viewed as an additional measure of evaluation and is also helpful in designing methods that account for the clinical prior such as association of certain areas in a brain to a particular cognitive task or connectivity of some brain regions via neural fibres. We formulate our method as a large-scale optimization problem to solve a constrained matrix factorization. Finding an optimal solution of the large-scale matrix factorization renders off-the-shelf solver computationally prohibitive; therefore, we designed an efficient algorithm based on the proximal method to address the computational bottle-neck of the optimization problem. Our formulation is readily extended for different scenarios such as cases where a large cohort of subjects has uncertain or no class labels (semi-supervised learning) or a case where each subject has a battery of imaging channels (multi-channel), \etc. We show that by using various notions of sparsity as feasible sets of the optimization problem, we can encode different forms of prior knowledge ranging from brain parcellation to brain connectivity

Neuroimaging Feature Extraction using a Neural Network Classifier for Imaging Genetics

A major issue in the association of genes to neuroimaging phenotypes is the high dimension of both genetic data and neuroimaging data. In this article, we tackle the latter problem with an eye toward developing solutions that are relevant for disease prediction. Supported by a vast literature on the predictive power of neural networks, our proposed solution uses neural networks to extract from neuroimaging data features that are relevant for predicting Alzheimer's Disease (AD) for subsequent relation to genetics. Our neuroimaging-genetic pipeline is comprised of image processing, neuroimaging feature extraction and genetic association steps. We propose a neural network classifier for extracting neuroimaging features that are related with disease and a multivariate Bayesian group sparse regression model for genetic association. We compare the predictive power of these features to expert selected features and take a closer look at the SNPs identified with the new neuroimaging features.Comment: Under revie

Phonatory and articulatory representations of speech production in cortical and subcortical fMRI responses

Speaking involves coordination of multiple neuromotor systems, including respiration, phonation and articulation. Developing non-invasive imaging methods to study how the brain controls these systems is critical for understanding the neurobiology of speech production. Recent models and animal research suggest that regions beyond the primary motor cortex (M1) help orchestrate the neuromotor control needed for speaking, including cortical and sub-cortical regions. Using contrasts between speech conditions with controlled respiratory behavior, this fMRI study investigates articulatory gestures involving the tongue, lips and velum (i.e., alveolars versus bilabials, and nasals versus orals), and phonatory gestures (i.e., voiced versus whispered speech). Multivariate pattern analysis (MVPA) was used to decode articulatory gestures in M1, cerebellum and basal ganglia. Furthermore, apart from confirming the role of a mid-M1 region for phonation, we found that a dorsal M1 region, linked to respiratory control, showed significant differences for voiced compared to whispered speech despite matched lung volume observations. This region was also functionally connected to tongue and lip M1 seed regions, underlying its importance in the coordination of speech. Our study confirms and extends current knowledge regarding the neural mechanisms underlying neuromotor speech control, which hold promise to study neural dysfunctions involved in motor-speech disorders non-invasively.Tis work was supported by the Spanish Ministry of Economy and Competitiveness through the Juan de la Cierva Fellowship (FJCI-2015-26814), and the Ramon y Cajal Fellowship (RYC-2017- 21845), the Spanish State Research Agency through the BCBL “Severo Ochoa” excellence accreditation (SEV-2015-490), the Basque Government (BERC 2018- 2021) and the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant (No 799554).info:eu-repo/semantics/publishedVersio