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Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits.
Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium imaging of a local microcircuit and mesoscopic widefield calcium imaging of the entire cortical mantle in awake mice. Our multi-scale approach involves a microscope with an orthogonal axis design where the mesoscopic objective is oriented above the brain and the two-photon objective is oriented horizontally, with imaging performed through a microprism. We also introduce a viral transduction method for robust and widespread gene delivery in the mouse brain. These approaches allow us to identify the behavioral state-dependent functional connectivity of pyramidal neurons and vasoactive intestinal peptide-expressing interneurons with long-range cortical networks. Our imaging system provides a powerful strategy for investigating cortical architecture across a wide range of spatial scales
Disentangling causal webs in the brain using functional Magnetic Resonance Imaging: A review of current approaches
In the past two decades, functional Magnetic Resonance Imaging has been used
to relate neuronal network activity to cognitive processing and behaviour.
Recently this approach has been augmented by algorithms that allow us to infer
causal links between component populations of neuronal networks. Multiple
inference procedures have been proposed to approach this research question but
so far, each method has limitations when it comes to establishing whole-brain
connectivity patterns. In this work, we discuss eight ways to infer causality
in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality,
Likelihood Ratios, LiNGAM, Patel's Tau, Structural Equation Modelling, and
Transfer Entropy. We finish with formulating some recommendations for the
future directions in this area
Improving Reliability of Subject-Level Resting-State fMRI Parcellation with Shrinkage Estimators
A recent interest in resting state functional magnetic resonance imaging
(rsfMRI) lies in subdividing the human brain into anatomically and functionally
distinct regions of interest. For example, brain parcellation is often used for
defining the network nodes in connectivity studies. While inference has
traditionally been performed on group-level data, there is a growing interest
in parcellating single subject data. However, this is difficult due to the low
signal-to-noise ratio of rsfMRI data, combined with typically short scan
lengths. A large number of brain parcellation approaches employ clustering,
which begins with a measure of similarity or distance between voxels. The goal
of this work is to improve the reproducibility of single-subject parcellation
using shrinkage estimators of such measures, allowing the noisy
subject-specific estimator to "borrow strength" in a principled manner from a
larger population of subjects. We present several empirical Bayes shrinkage
estimators and outline methods for shrinkage when multiple scans are not
available for each subject. We perform shrinkage on raw intervoxel correlation
estimates and use both raw and shrinkage estimates to produce parcellations by
performing clustering on the voxels. Our proposed method is agnostic to the
choice of clustering method and can be used as a pre-processing step for any
clustering algorithm. Using two datasets---a simulated dataset where the true
parcellation is known and is subject-specific and a test-retest dataset
consisting of two 7-minute rsfMRI scans from 20 subjects---we show that
parcellations produced from shrinkage correlation estimates have higher
reliability and validity than those produced from raw estimates. Application to
test-retest data shows that using shrinkage estimators increases the
reproducibility of subject-specific parcellations of the motor cortex by up to
30%.Comment: body 21 pages, 11 figure
Human brain mapping: a systematic comparison of parcellation methods for the human cerebral cortex
The macro-connectome elucidates the pathways through which brain regions are structurally connected or functionally coupled to perform a specific cognitive task. It embodies the notion of representing and understanding all connections within the brain as a network, while the subdivision of the brain into interacting functional units is inherent in its architecture. As a result, the definition of network nodes is one of the most critical steps in connectivity network analysis. Although brain atlases obtained from cytoarchitecture or anatomy have long been used for this task, connectivity-driven methods have arisen only recently, aiming to delineate more homogeneous and functionally coherent regions. This study provides a systematic comparison between anatomical, connectivity-driven and random parcellation methods proposed in the thriving field of brain parcellation. Using resting-state functional MRI data from the Human Connectome Project and a plethora of quantitative evaluation techniques investigated in the literature, we evaluate 10 subject-level and 24 groupwise parcellation methods at different resolutions. We assess the accuracy of parcellations from four different aspects: (1) reproducibility across different acquisitions and groups, (2) fidelity to the underlying connectivity data, (3) agreement with fMRI task activation, myelin maps, and cytoarchitectural areas, and (4) network analysis. This extensive evaluation of different parcellations generated at the subject and group level highlights the strengths and shortcomings of the various methods and aims to provide a guideline for the choice of parcellation technique and resolution according to the task at hand. The results obtained in this study suggest that there is no optimal method able to address all the challenges faced in this endeavour simultaneously
Which fMRI clustering gives good brain parcellations?
International audienceAnalysis and interpretation of neuroimaging data often require one to divide the brain into a number of regions, or parcels, with homogeneous characteristics, be these regions defined in the brain volume or on on the cortical surface. While predefined brain atlases do not adapt to the signal in the individual subjects images, parcellation approaches use brain activity (e.g. found in some functional contrasts of interest) and clustering techniques to define regions with some degree of signal homogeneity. In this work, we address the question of which clustering technique is appropriate and how to optimize the corresponding model. We use two principled criteria: goodness of fit (accuracy), and reproducibility of the parcellation across bootstrap samples. We study these criteria on both simulated and two task-based functional Magnetic Resonance Imaging datasets for the Ward, spectral and K-means clustering algorithms. We show that in general Ward's clustering performs better than alternative methods with regard to reproducibility and accuracy and that the two criteria diverge regarding the preferred models (reproducibility leading to more conservative solutions), thus deferring the practical decision to a higher level alternative, namely the choice of a trade-off between accuracy and stability
Functional Brain Organization in Space and Time
The brain is a network functionally organized at many spatial and temporal scales. To understand how the brain processes information, controls behavior and dynamically adapts to an ever-changing environment, it is critical to have a comprehensive description of the constituent elements of this network and how relationships between these elements may change over time. Decades of lesion studies, anatomical tract-tracing, and electrophysiological recording have given insight into this functional organization. Recently, however, resting state functional magnetic resonance imaging (fMRI) has emerged as a powerful tool for whole-brain non-invasive measurement of spontaneous neural activity in humans, giving ready access to macroscopic scales of functional organization previously much more difficult to obtain. This thesis aims to harness the unique combination of spatial and temporal resolution provided by functional MRI to explore the spatial and temporal properties of the functional organization of the brain. First, we establish an approach for defining cortical areas using transitions in correlated patterns of spontaneous BOLD activity (Chapter 2). We then propose and apply measures of internal and external validity to evaluate the credibility of the areal parcellation generated by this technique (Chapter 3). In chapter 4, we extend the study of functional brain organization to a highly sampled individual. We describe the idiosyncratic areal and systems-level organization of the individual relative to a standard group-average description. Further, we develop a model describing the reliability of BOLD correlation estimates across days that accounts for relevant sources of variability. Finally, in Chapter 5, we examine whether BOLD correlations meaningfully vary over the course of single resting-state scans
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