2,484 research outputs found
Learning and comparing functional connectomes across subjects
Functional connectomes capture brain interactions via synchronized
fluctuations in the functional magnetic resonance imaging signal. If measured
during rest, they map the intrinsic functional architecture of the brain. With
task-driven experiments they represent integration mechanisms between
specialized brain areas. Analyzing their variability across subjects and
conditions can reveal markers of brain pathologies and mechanisms underlying
cognition. Methods of estimating functional connectomes from the imaging signal
have undergone rapid developments and the literature is full of diverse
strategies for comparing them. This review aims to clarify links across
functional-connectivity methods as well as to expose different steps to perform
a group study of functional connectomes
Extracting brain regions from rest fMRI with Total-Variation constrained dictionary learning
International audienceSpontaneous brain activity reveals mechanisms of brain function and dysfunction. Its population-level statistical analysis based on functional images often relies on the de nition of brain regions that must summarize e ciently the covariance structure between the multiple brain networks. In this paper, we extend a network-discovery approach, namely dictionary learning, to readily extract brain regions. To do so, we intro duce a new tool drawing from clustering and linear decomposition methods by carefully crafting a penalty. Our approach automatically extracts regions from rest fMRI that better explain the data and are more stable across subjects than reference decomposition or clustering methods
Compressed Online Dictionary Learning for Fast fMRI Decomposition
We present a method for fast resting-state fMRI spatial decomposi-tions of
very large datasets, based on the reduction of the temporal dimension before
applying dictionary learning on concatenated individual records from groups of
subjects. Introducing a measure of correspondence between spatial
decompositions of rest fMRI, we demonstrates that time-reduced dictionary
learning produces result as reliable as non-reduced decompositions. We also
show that this reduction significantly improves computational scalability
Cohort-level brain mapping: learning cognitive atoms to single out specialized regions
International audienceFunctional Magnetic Resonance Imaging (fMRI) studies map the human brain by testing the response of groups of individuals to carefully-crafted and contrasted tasks in order to delineate specialized brain regions and networks. The number of functional networks extracted is limited by the number of subject-level contrasts and does not grow with the cohort. Here, we introduce a new group-level brain mapping strategy to differentiate many regions reflecting the variety of brain network configurations observed in the population. Based on the principle of functional segregation, our approach singles out functionally-specialized brain regions by learning group-level functional profiles on which the response of brain regions can be represented sparsely. We use a dictionary-learning formulation that can be solved efficiently with on-line algorithms, scaling to arbitrary large datasets. Importantly, we model inter-subject correspondence as structure imposed in the estimated functional profiles, integrating a structure-inducing regularization with no additional computational cost. On a large multi-subject study, our approach extracts a large number of brain networks with meaningful functional profiles
Machine Learning for Neuroimaging with Scikit-Learn
Statistical machine learning methods are increasingly used for neuroimaging
data analysis. Their main virtue is their ability to model high-dimensional
datasets, e.g. multivariate analysis of activation images or resting-state time
series. Supervised learning is typically used in decoding or encoding settings
to relate brain images to behavioral or clinical observations, while
unsupervised learning can uncover hidden structures in sets of images (e.g.
resting state functional MRI) or find sub-populations in large cohorts. By
considering different functional neuroimaging applications, we illustrate how
scikit-learn, a Python machine learning library, can be used to perform some
key analysis steps. Scikit-learn contains a very large set of statistical
learning algorithms, both supervised and unsupervised, and its application to
neuroimaging data provides a versatile tool to study the brain.Comment: Frontiers in neuroscience, Frontiers Research Foundation, 2013, pp.1
Region segmentation for sparse decompositions: better brain parcellations from rest fMRI
International audienceFunctional Magnetic Resonance Images acquired during resting-state provide information about the functional organization of the brain through measuring correlations between brain areas. Independent components analysis is the reference approach to estimate spatial components from weakly structured data such as brain signal time courses; each of these components may be referred to as a brain network and the whole set of components can be conceptualized as a brain functional atlas. Recently, new methods using a sparsity prior have emerged to deal with low signal-to-noise ratio data. However, even when using sophisticated priors, the results may not be very sparse and most often do not separate the spatial components into brain regions. This work presents post-processing techniques that automatically sparsify brain maps and separate regions properly using geometric operations, and compares these techniques according to faithfulness to data and stability metrics. In particular, among threshold-based approaches, hysteresis thresholding and random walker segmentation, the latter improves significantly the stability of both dense and sparse models
Testing for Differences in Gaussian Graphical Models: Applications to Brain Connectivity
Functional brain networks are well described and estimated from data with
Gaussian Graphical Models (GGMs), e.g. using sparse inverse covariance
estimators. Comparing functional connectivity of subjects in two populations
calls for comparing these estimated GGMs. Our goal is to identify differences
in GGMs known to have similar structure. We characterize the uncertainty of
differences with confidence intervals obtained using a parametric distribution
on parameters of a sparse estimator. Sparse penalties enable statistical
guarantees and interpretable models even in high-dimensional and low-sample
settings. Characterizing the distributions of sparse models is inherently
challenging as the penalties produce a biased estimator. Recent work invokes
the sparsity assumptions to effectively remove the bias from a sparse estimator
such as the lasso. These distributions can be used to give confidence intervals
on edges in GGMs, and by extension their differences. However, in the case of
comparing GGMs, these estimators do not make use of any assumed joint structure
among the GGMs. Inspired by priors from brain functional connectivity we derive
the distribution of parameter differences under a joint penalty when parameters
are known to be sparse in the difference. This leads us to introduce the
debiased multi-task fused lasso, whose distribution can be characterized in an
efficient manner. We then show how the debiased lasso and multi-task fused
lasso can be used to obtain confidence intervals on edge differences in GGMs.
We validate the techniques proposed on a set of synthetic examples as well as
neuro-imaging dataset created for the study of autism
Impact of perceptual learning on resting-state fMRI connectivity: A supervised classification study
International audiencePerceptual learning sculpts ongoing brain activity [1]. This finding has been observed by statistically comparing the functional connectivity (FC) patterns computed from resting-state functional MRI (rs-fMRI) data recorded before and after intensive training to a visual attention task. Hence, functional connectivity serves a dynamic role in brain function, supporting the consolidation of previous experience. Following this line of research, we trained three groups of individuals to a visual discrimination task during a magneto-encephalography (MEG) experiment [2]. The same individuals were then scanned in rs-fMRI. Here, in a supervised classification framework, we demonstrate that FC metrics computed on rs-fMRI data are able to predict the type of training the participants received. On top of that, we show that the prediction accuracies based on tangent embedding FC measure outperform those based on our recently developed multivariate wavelet-based Hurst exponent estimator [3], which captures low frequency fluctuations in ongoing brain activity too
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