scholarly journals Data and model considerations for estimating time-varying functional connectivity in fMRI

2021 ◽  
Author(s):  
Christine Ahrends ◽  
Angus Stevner ◽  
Usama Pervaiz ◽  
Morten L. Kringelbach ◽  
Peter Vuust ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Resting State Fmri ◽  
Temporal Changes ◽  
Model Parameters ◽  
Time Varying ◽  
Time Courses ◽  
Session State ◽  
Temporal Sequences ◽  
The Brain ◽  
Practical Recommendations

Functional connectivity (FC) in the brain has been shown to exhibit subtle but reliable modulations within a session. One way of estimating time-varying FC is by using state-based models that describe fMRI time series as temporal sequences of states, each with an associated, characteristic pattern of FC. However, the estimation of these models from data sometimes fails to capture changes in a meaningful way, such that the model estimation assigns entire sessions (or the largest part of them) to a single state, therefore failing to capture within-session state modulations effectively; we refer to this phenomenon as the model becoming static, or model stasis. Here, we aim to quantify how the nature of the data and the choice of model parameters affect the model's ability to detect temporal changes in FC using both simulated fMRI time courses and resting state fMRI data. We show that large between-subject FC differences can overwhelm subtler within-session modulations, causing the model to become static. Further, the choice of parcellation can also affect the model's ability to detect temporal changes. We finally show that the model often becomes static when the number of free parameters that need to be estimated is high and the number of observations available for this estimation is low in comparison. Based on these findings, we derive a set of practical recommendations for time-varying FC studies, in terms of preprocessing, parcellation and complexity of the model.

Inter-Hemispherical Investigations on the Functional Connectivity in Controls and Autism Spectrum Using Resting State fMRI

2020 ◽  
pp. 169-186
Author(s):  
S. Vidhusha ◽  
A. Kavitha
Keyword(s):  
Functional Connectivity ◽  
Granger Causality ◽  
Resting State ◽  
Cognitive Task ◽  
Resting State Fmri ◽  
Autism Spectrum ◽  
Control Group ◽  
Neural Connectivity ◽  
Activation Patterns ◽  
The Brain

Autism spectrum disorders are connected with disturbances of neural connectivity. Functional connectivity is typically examined during a cognitive task, but also exists in the absence of a task. While a number of studies have performed functional connectivity analysis to differentiate controls and autism individuals, this work focuses on analyzing the brain activation patterns not only between controls and autistic subjects, but also analyses the brain behaviour present within autism spectrum. This can bring out more intuitive ways to understand that autism individuals differ individually. This has been performed between autism group relative to the control group using inter-hemispherical analysis. Indications of under connectivity were exhibited by the Granger Causality (GC) and Conditional Granger Causality (CGC) in autistic group. Results show that as connectivity decreases, the GC and CGC values also get decreased. Further, to demark the differences present within the spectrum of autistic individuals, GC and CGC values have been calculated.

scholarly journals Identifying optimal working points of individual Virtual Brains: A large-scale brain network modelling study

2020 ◽  
Author(s):  
Paul Triebkorn ◽  
Joelle Zimmermann ◽  
Leon Stefanovski ◽  
Dipanjan Roy ◽  
Ana Solodkin ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Brain Function ◽  
Large Scale ◽  
Brain Activity ◽  
Brain Network ◽  
Model Parameters ◽  
Network Modelling ◽  
Neural Populations ◽  
Global Coupling ◽  
The Brain

AbstractUsing The Virtual Brain (TVB, thevirtualbrian.org) simulation platform, we explored for 50 individual adult human brains (ages 18-80), how personalized connectome based brain network modelling captures various empirical observations as measured by functional magnetic resonance imaging (fMRI) and electroencephalography (EEG). We compare simulated activity based on individual structural connectomes (SC) inferred from diffusion weighted imaging with fMRI and EEG in the resting state. We systematically explore the role of the following model parameters: conduction velocity, global coupling and graph theoretical features of individual SC. First, a subspace of the parameter space is identified for each subject that results in realistic brain activity, i.e. reproducing the following prominent features of empirical EEG-fMRI activity: topology of resting-state fMRI functional connectivity (FC), functional connectivity dynamics (FCD), electrophysiological oscillations in the delta (3-4 Hz) and alpha (8-12 Hz) frequency range and their bimodality, i.e. low and high energy modes. Interestingly, FCD fit, bimodality and static FC fit are highly correlated. They all show their optimum in the same range of global coupling. In other words, only when our local model is in a bistable regime we are able to generate switching of modes in our global network. Second, our simulations reveal the explicit network mechanisms that lead to electrophysiological oscillations, their bimodal behaviour and inter-regional differences. Third, we discuss biological interpretability of the Stefanescu-Jirsa-Hindmarsh-Rose-3D model when embedded inside the large-scale brain network and mechanisms underlying the emergence of bimodality of the neural signal.With the present study, we set the cornerstone for a systematic catalogue of spatiotemporal brain activity regimes generated with the connectome-based brain simulation platform The Virtual Brain.Author SummaryIn order to understand brain dynamics we use numerical simulations of brain network models. Combining the structural backbone of the brain, that is the white matter fibres connecting distinct regions in the grey matter, with dynamical systems describing the activity of neural populations we are able to simulate brain function on a large scale. In order to make accurate prediction with this network, it is crucial to determine optimal model parameters. We here use an explorative approach to adjust model parameters to individual brain activity, showing that subjects have their own optimal point in the parameter space, depending on their brain structure and function. At the same time, we investigate the relation between bistable phenomena on the scale of neural populations and the changed in functional connectivity on the brain network scale. Our results are important for future modelling approaches trying to make accurate predictions of brain function.

scholarly journals Nuisance Effects and the Limitations of Nuisance Regression in Dynamic Functional Connectivity fMRI

2018 ◽  
Author(s):  
Alican Nalci ◽  
Bhaskar D. Rao ◽  
Thomas T. Liu
Keyword(s):  
Functional Connectivity ◽  
Resting State Fmri ◽  
Brain Regions ◽  
Blood Oxygenation ◽  
Dynamic Functional Connectivity ◽  
Temporal Fluctuations ◽  
Before And After ◽  
The Difference ◽  
Time Courses ◽  
The Relationship

AbstractIn resting-state fMRI, dynamic functional connectivity (DFC) measures are used to characterize temporal changes in the brain’s intrinsic functional connectivity. A widely used approach for DFC estimation is the computation of the sliding window correlation between blood oxygenation level dependent (BOLD) signals from different brain regions. Although the source of temporal fluctuations in DFC estimates remains largely unknown, there is growing evidence that they may reflect dynamic shifts between functional brain networks. At the same time, recent findings suggest that DFC estimates might be prone to the influence of nuisance factors such as the physiological modulation of the BOLD signal. Therefore, nuisance regression is used in many DFC studies to regress out the effects of nuisance terms prior to the computation of DFC estimates. In this work we examined the relationship between DFC estimates and nuisance factors. We found that DFC estimates were significantly correlated with temporal fluctuations in the magnitude (norm) of various nuisance regressors, with significant correlations observed in the majority (76%) of the cases examined. Significant correlations between the DFC estimates and nuisance regressor norms were found even when the underlying correlations between the nuisance and fMRI time courses were relatively small. We then show that nuisance regression does not eliminate the relationship between DFC estimates and nuisance norms, with significant correlations observed in the majority (71%) of the cases examined after nuisance regression. We present theoretical bounds on the difference between DFC estimates obtained before and after nuisance regression and relate these bounds to limitations in the efficacy of nuisance regression with regards to DFC estimates.

Identification of Brain Functional Networks Using a Model-Based Approach

2019 ◽  
Vol 34 (08) ◽  
pp. 2057004
Author(s):  
Vangelis P. Oikonomou ◽  
Konstantinos Blekas ◽  
Loukas Astrakas
Keyword(s):  
Time Series ◽  
Resting State ◽  
Probabilistic Method ◽  
Resting State Fmri ◽  
Model Parameters ◽  
Resting State Networks ◽  
Model Based ◽  
Functional Brain Networks ◽  
Regression Mixture ◽  
The Brain

Functional MRI (fMRI) is a valuable brain imaging technique. A significant problem, when analyzing fMRI time series, is the finding of functional brain networks when the brain is at rest, i.e. no external stimulus is applied to the subject. In this work, we present a probabilistic method to estimate the Resting State Networks (RSNs) using a model-based approach. More specifically, RSNs are assumed to be the result of a clustering procedure. In order to perform the clustering, a mixture of regression models are used. Furthermore, special care has been given in order to incorporate important functionalities, such as spatial and embedded sparsity enforcing properties, through the use of informative priors over the model parameters. Another interesting feature of the proposed scheme is the flexibility to handle all the brain time series at once, allowing more robust solutions. We provide comparative experimental results, using an artificial fMRI dataset and two real resting state fMRI datasets, that empirically illustrate the efficiency of the proposed regression mixture model.

scholarly journals Individual Thresholding of Voxel-based Functional Connectivity Maps

2015 ◽  
Vol 54 (03) ◽  
pp. 227-231 ◽  
Author(s):  
F. Baglio ◽  
M. M. Laganà ◽  
M. G. Preti ◽  
P. Cecconi ◽  
M. Clerici ◽  
...  
Keyword(s):  
Time Series ◽  
Functional Connectivity ◽  
Threshold Value ◽  
Resting State Fmri ◽  
Posterior Cingulate Cortex ◽  
Single Subject ◽  
Random Errors ◽  
Global Threshold ◽  
Correlation Threshold ◽  
The Brain

SummaryIntroduction: This article is part of the Focus Theme of Methods of Information in Medicine on “Biosignal Interpretation: Advanced Methods for Neural Signals and Images”.Background: Voxel-based functional connectivity analysis is a common method for resting state fMRI data. However, correlations between the seed and other brain voxels are corrupted by random estimate errors yielding false connections within the functional connectivity map (FCmap). These errors must be taken into account for a correct interpretation of single-subject results.Objectives: We estimated the statistical range of random errors and propose two methods for an individual setting of correlation threshold for FCmaps.Methods: We assessed the amount of random errors by means of surrogate time series and described its distribution within the brain. On the basis of these results, the FCmaps of the posterior cingulate cortex (PCC) from 15 healthy subjects were thresholded with two innovative methods: the first one consisted in the computation of a unique (global) threshold value to be applied to all brain voxels, while the second method is to set a different (local) threshold of each voxel of the FCmap.Results: The distribution of random errors within the brain was observed to be homogeneous and, after thresholding with both methods, the default mode network areas were well identifiable. The two methods yielded similar results, however the application of a global threshold to all brain voxels requires a reduced computational load. The inter-subject variability of the global threshold was observed to be very low and not correlated with age. Global threshold values are also almost independent from the number of surrogates used for their computation, so the analyses can be optimized using a reduced number of surrogate time series.Conclusions: We demonstrated the efficacy of FCmaps thresholding based on random error estimation. This method can be used for a reliable single-subject analysis and could also be applied in clinical setting, to compute individual measures of disease progression or quantitative response to pharmacological or rehabilitation treatments.

scholarly journals Whole-brain dynamics in aging: disruptions in functional connectivity and the role of the rich club

2020 ◽  
Author(s):  
Anira Escrichs ◽  
Carles Biarnes ◽  
Josep Garre-Olmo ◽  
José Manuel Fernández-Real ◽  
Rafel Ramos ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Resting State Fmri ◽  
Brain Dynamics ◽  
Whole Brain ◽  
Rich Club ◽  
Brain Functional Network ◽  
Age Related ◽  
Age Range ◽  
The Brain

AbstractNormal aging causes disruptions in the brain that can lead to cognitive decline. Resting-state fMRI studies have found significant age-related alterations in functional connectivity across various networks. Nevertheless, most of the studies have focused mainly on static functional connectivity. Studying the dynamics of resting-state brain activity across the whole-brain functional network can provide a better characterization of age-related changes. Here we employed two data-driven whole-brain approaches based on the phase synchronization of blood-oxygen-level-dependent (BOLD) signals to analyze resting-state fMRI data from 620 subjects divided into two groups (‘middle-age group’ (n=310); age range, 50-65 years vs. ‘older group’ (n=310); age range, 66-91 years). Applying the Intrinsic-Ignition Framework to assess the effect of spontaneous local activation events on local-global integration, we found that the older group showed higher intrinsic ignition across the whole-brain functional network, but lower metastability. Using Leading Eigenvector Dynamics Analysis, we found that the older group showed reduced ability to access a metastable substate that closely overlaps with the so-called rich club. These findings suggest that functional whole-brain dynamics are altered in aging, probably due to a deficiency in a metastable substate that is key for efficient global communication in the brain.

scholarly journals Brain activity fluctuations propagate as waves traversing the cortical hierarchy

2020 ◽  
Author(s):  
Yameng Gu ◽  
Lucas E. Sainburg ◽  
Sizhe Kuang ◽  
Feng Han ◽  
Jack W. Williams ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Spontaneous Activity ◽  
Resting State ◽  
Brain Activity ◽  
Resting State Fmri ◽  
Hierarchical Organization ◽  
Subcortical Structures ◽  
Cortical Hierarchy ◽  
Neural Origin ◽  
The Brain

AbstractThe brain exhibits highly organized patterns of spontaneous activity as measured by resting-state fMRI fluctuations that are being widely used to assess the brain’s functional connectivity. Some evidence suggests that spatiotemporally coherent waves are a core feature of spontaneous activity that shapes functional connectivity, though this has been difficult to establish using fMRI given the temporal constraints of the hemodynamic signal. Here we investigated the structure of spontaneous waves in human fMRI and monkey electrocorticography. In both species, we found clear, repeatable, and directionally constrained activity waves coursed along a spatial axis approximately representing cortical hierarchical organization. These cortical propagations were closely associated with activity changes in distinct subcortical structures, particularly those related to arousal regulation, and modulated across different states of vigilance. The findings demonstrate a neural origin of spatiotemporal fMRI wave propagation at rest and link it to the principal gradient of resting-state fMRI connectivity.

scholarly journals Increased Within-Network Functional Connectivity May Predict NEDA Status in Fingolimod-Treated MS Patients

2021 ◽  
Vol 12 ◽  
Author(s):  
Claudia Piervincenzi ◽  
Nikolaos Petsas ◽  
Laura De Giglio ◽  
Maurizio Carmellini ◽  
Costanza Giannì ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Disease Activity ◽  
Resting State Fmri ◽  
Short Term ◽  
Term Outcome ◽  
Default Mode ◽  
Functional Changes ◽  
Functional Reorganization ◽  
Brain Functional Connectivity ◽  
The Brain

Only a few studies have evaluated the brain functional changes associated with disease-modifying therapies (DMTs) in multiple sclerosis (MS), though none used a composite measure of clinical and MRI outcomes to evaluate DMT-related brain functional connectivity (FC) measures predictive of short-term outcome. Therefore, we investigated the following: (1) baseline FC differences between patients who showed evidence of disease activity after a specific DMT and those who did not; (2) DMT-related effects on FC, and; (3) possible relationships between DMT-related FC changes and changes in performance. We used a previously analyzed dataset of 30 relapsing MS patients who underwent fingolimod treatment for 6 months and applied the “no evidence of disease activity” (NEDA-3) status as a clinical response indicator of treatment efficacy. Resting-state fMRI data were analyzed to obtain within- and between-network FC measures. After therapy, 14 patients achieved NEDA-3 status (hereinafter NEDA), while 16 did not (EDA). The two groups significantly differed at baseline, with the NEDA group having higher within-network FC in the anterior and posterior default mode, auditory, orbitofrontal, and right frontoparietal networks than the EDA. After therapy, NEDA showed significantly reduced within-network FC in the posterior default mode and left frontoparietal networks and increased between-network FC in the posterior default mode/orbitofrontal networks; they also showed PASAT improvement, which was correlated with greater within-network FC decrease in the posterior default mode network and with greater between-network FC increase. No significant longitudinal FC changes were found in the EDA. Taken together, these findings suggest that NEDA status after fingolimod is related to higher within-network FC at baseline and to a consistent functional reorganization after therapy.

Abstract 2713: Functional Recovery Associated with Connectivity Changes in Contralesional Hemisphere after Severe Transient Stroke.

Stroke ◽  
2012 ◽  
Vol 43 (suppl_1) ◽  
Author(s):  
WOO HYUN SHIM ◽  
Bruce Rosen ◽  
Jaeseung Jeong ◽  
Young Kim
Keyword(s):  
Functional Connectivity ◽  
Functional Recovery ◽  
Brain Connectivity ◽  
Control Group ◽  
Sprague Dawley ◽  
Sensorimotor Deficit ◽  
Stroke Models ◽  
Time Courses ◽  
The Right ◽  
The Brain

Stroke impairs connections in the brain system, commonly resulting in significant sensorimotor deficits. Some degree of functional recovery typically occurs even after a severe stroke, yet changes in the brain connectivity that underlie such recovery are poorly understood. In this study, using rat stroke models, we monitored functional connectivity when the sensorimotor deficit recovered after a severe ischemic stroke (defined DWI by more than 15% of the entire brain volume). We used seven Sprague-Dawley rats (∼350g), which showed nearly full recovery of both motor and sensory functions approximately 180 days after 90 min occlusion of the right middle cerebral artery. Six healthy age controlled rats were used for the control group. BOLD MRI time courses during rest (10min, TR=1s, 9 slices) were collected. Both the seed-voxel analysis and the ROI-based analysis were performed, in which seed voxels were selected in the left S1FL, and multiple ROIs were placed over the somatosensory regions. Stroke rats showed the markedly decreased functional connectivity in the ipsilesional side (right) for both voxelwise and ROI-based methods. Interestingly, in contralesional (non-stroke) side (left), the voxelwise connectivity spatially expanded into the entire cortical area. The cross-correlation coefficient values between ROI’s slightly increased in the contralesional hemisphere compared to the control rats. In conclusion, we demonstrated that the restoration of sensorimotor function is associated more with the increase and spatial expansion of functional connectivity within the contralesional than the ipsilesional hemisphere.

Sign in / Sign up

Export Citation Format

Share Document