25 research outputs found
A blind deconvolution approach to recover effective connectivity brain networks from resting state fMRI data
A great improvement to the insight on brain function that we can get from
fMRI data can come from effective connectivity analysis, in which the flow of
information between even remote brain regions is inferred by the parameters of
a predictive dynamical model. As opposed to biologically inspired models, some
techniques as Granger causality (GC) are purely data-driven and rely on
statistical prediction and temporal precedence. While powerful and widely
applicable, this approach could suffer from two main limitations when applied
to BOLD fMRI data: confounding effect of hemodynamic response function (HRF)
and conditioning to a large number of variables in presence of short time
series. For task-related fMRI, neural population dynamics can be captured by
modeling signal dynamics with explicit exogenous inputs; for resting-state fMRI
on the other hand, the absence of explicit inputs makes this task more
difficult, unless relying on some specific prior physiological hypothesis. In
order to overcome these issues and to allow a more general approach, here we
present a simple and novel blind-deconvolution technique for BOLD-fMRI signal.
Coming to the second limitation, a fully multivariate conditioning with short
and noisy data leads to computational problems due to overfitting. Furthermore,
conceptual issues arise in presence of redundancy. We thus apply partial
conditioning to a limited subset of variables in the framework of information
theory, as recently proposed. Mixing these two improvements we compare the
differences between BOLD and deconvolved BOLD level effective networks and draw
some conclusions
Retrieving the hemodynamic response function in resting state fMRI: methodology and application
In this paper we present a procedure to retrieve the hemodynamic response function (HRF) from resting state functional magnetic resonance imaging (fMRI) data. The fundamentals of the procedures are further validated by considering simultaneous electroencephalographic (EEG) recordings. The typical HRF shape at rest for a group of healthy subject is presented. Then we present the modifications to the shape of the HRF at rest following two physiological modulations: eyes open versus eyes closed and propofol-induced modulations of consciousness
FMRI hemodynamic response function (HRF) as a novel marker of brain function: applications for understanding obsessive-compulsive disorder pathology and treatment response
The hemodynamic response function (HRF) represents the transfer function linking neural activity with the functional MRI (fMRI) signal, modeling neurovascular coupling. Since HRF is influenced by non-neural factors, to date it has largely been considered as a confound or has been ignored in many analyses. However, underlying biophysics suggests that the HRF may contain meaningful correlates of neural activity, which might be unavailable through conventional fMRI metrics. Here, we estimated the HRF by performing deconvolution on resting-state fMRI data from a longitudinal sample of 25 healthy controls scanned twice and 44 adults with obsessive-compulsive disorder (OCD) before and after 4-weeks of intensive cognitive-behavioral therapy (CBT). HRF response height, time-to-peak and full-width at half-maximum (FWHM) in OCD were abnormal before treatment and normalized after treatment in regions including the caudate. Pre-treatment HRF predicted treatment outcome (OCD symptom reduction) with 86.4% accuracy, using machine learning. Pre-treatment HRF response height in the caudate head and time-to-peak in the caudate tail were top-predictors of treatment response. Time-to-peak in the caudate tail, a region not typically identified in OCD studies using conventional fMRI activation or connectivity measures, may carry novel importance. Additionally, pre-treatment response height in caudate head predicted post-treatment OCD severity (R = -0.48, P = 0.001), and was associated with treatment-related OCD severity changes (R = -0.44, P = 0.0028), underscoring its relevance. With HRF being a reliable marker sensitive to brain function, OCD pathology, and intervention-related changes, these results could guide future studies towards novel discoveries not possible through conventional fMRI approaches like standard BOLD activation or connectivity
Lagged and instantaneous dynamical influences related to brain structural connectivity
Contemporary neuroimaging methods can shed light on the basis of human neural
and cognitive specializations, with important implications for neuroscience and
medicine. Different MRI acquisitions provide different brain networks at the
macroscale; whilst diffusion-weighted MRI (dMRI) provides a structural
connectivity (SC) coincident with the bundles of parallel fibers between brain
areas, functional MRI (fMRI) accounts for the variations in the
blood-oxygenation-level-dependent T2* signal, providing functional connectivity
(FC).Understanding the precise relation between FC and SC, that is, between
brain dynamics and structure, is still a challenge for neuroscience. To
investigate this problem, we acquired data at rest and built the corresponding
SC (with matrix elements corresponding to the fiber number between brain areas)
to be compared with FC connectivity matrices obtained by 3 different methods:
directed dependencies by an exploratory version of structural equation modeling
(eSEM), linear correlations (C) and partial correlations (PC). We also
considered the possibility of using lagged correlations in time series; so, we
compared a lagged version of eSEM and Granger causality (GC). Our results were
two-fold: firstly, eSEM performance in correlating with SC was comparable to
those obtained from C and PC, but eSEM (not C nor PC) provides information
about directionality of the functional interactions. Second, interactions on a
time scale much smaller than the sampling time, captured by instantaneous
connectivity methods, are much more related to SC than slow directed influences
captured by the lagged analysis. Indeed the performance in correlating with SC
was much worse for GC and for the lagged version of eSEM. We expect these
results to supply further insights to the interplay between SC and functional
patterns, an important issue in the study of brain physiology and function.Comment: Accepted and published in Frontiers in Psychology in its current
form. 27 pages, 1 table, 5 figures, 2 suppl. figure
Information flow between resting state networks
The resting brain dynamics self-organizes into a finite number of correlated
patterns known as resting state networks (RSNs). It is well known that
techniques like independent component analysis can separate the brain activity
at rest to provide such RSNs, but the specific pattern of interaction between
RSNs is not yet fully understood. To this aim, we propose here a novel method
to compute the information flow (IF) between different RSNs from resting state
magnetic resonance imaging. After haemodynamic response function blind
deconvolution of all voxel signals, and under the hypothesis that RSNs define
regions of interest, our method first uses principal component analysis to
reduce dimensionality in each RSN to next compute IF (estimated here in terms
of Transfer Entropy) between the different RSNs by systematically increasing k
(the number of principal components used in the calculation). When k = 1, this
method is equivalent to computing IF using the average of all voxel activities
in each RSN. For k greater than one our method calculates the k-multivariate IF
between the different RSNs. We find that the average IF among RSNs is
dimension-dependent, increasing from k =1 (i.e., the average voxels activity)
up to a maximum occurring at k =5 to finally decay to zero for k greater than
10. This suggests that a small number of components (close to 5) is sufficient
to describe the IF pattern between RSNs. Our method - addressing differences in
IF between RSNs for any generic data - can be used for group comparison in
health or disease. To illustrate this, we have calculated the interRSNs IF in a
dataset of Alzheimer's Disease (AD) to find that the most significant
differences between AD and controls occurred for k =2, in addition to AD
showing increased IF w.r.t. controls.Comment: 47 pages, 5 figures, 4 tables, 3 supplementary figures. Accepted for
publication in Brain Connectivity in its current for
Revisiting non-linear functional brain co-activations: directed, dynamic and delayed
The center stage of neuro-imaging is currently occupied by studies of
functional correlations between brain regions. These correlations define the
brain functional networks, which are the most frequently used framework to
represent and interpret a variety of experimental findings. In previous work we
first demonstrated that the relatively stronger BOLD activations contain most
of the information relevant to understand functional connectivity and
subsequent work confirmed that a large compression of the original signals can
be obtained without significant loss of information. In this work we revisit
the correlation properties of these epochs to define a measure of nonlinear
dynamic directed functional connectivity (nldFC) across regions of interest. We
show that the proposed metric provides at once, without extensive numerical
complications, directed information of the functional correlations, as well as
a measure of temporal lags across regions, overall offering a different
perspective in the analysis of brain co-activation patterns. In this paper we
provide for a proof of concept, based on replicating and completing existing
results on an Autism database, to discuss the main features and advantages of
the proposed strategy for the study of brain functional correlations. These
results show new interpretations of the correlations found on this sample.Comment: 12 pages, 8 figure
Beyond the “Pain Matrix,†inter-run synchronization during mechanical nociceptive stimulation
Pain is a complex experience that is thought to emerge from the activity of multiple brain areas, some of which are inconsistently detected using traditional fMRI analysis. One hypothesis is that the traditional analysis of pain-related cerebral responses, by relying on the correlation of a predictor and the canonical hemodynamic response function (HRF)- the general linear model (GLM)- may under-detect the activity of those areas involved in stimulus processing that do not present a canonical HRF. In this study, we employed an innovative data-driven processing approach- an inter-run synchronization (IRS) analysis- that has the advantage of not establishing any pre-determined predictor definition. With this method we were able to evidence the involvement of several brain regions that are not usually found when using predictor-based analysis. These areas are synchronized during the administration of mechanical punctate stimuli and are characterized by a BOLD response different from the canonical HRF. This finding opens to new approaches in the study of pain imaging
The confound of hemodynamic response function variability in human resting-state functional MRI studies
Functional magnetic resonance imaging (fMRI) is an indirect measure of neural activity with the hemodynamic response function (HRF) coupling it with unmeasured neural activity. The HRF, modulated by several non-neural factors, is variable across brain regions, individuals and populations. Yet, a majority of human resting-state fMRI connectivity studies continue to assume a non-variable HRF. In this article, with supportive prior evidence, we argue that HRF variability cannot be ignored as it substantially confounds within-subject connectivity estimates and between-subjects connectivity group differences. We also discuss its clinical relevance with connectivity impairments confounded by HRF aberrations in several disorders. We present limited data on HRF differences between women and men, which resulted in a 15.4% median error in functional connectivity estimates in a group-level comparison. We also discuss the implications of HRF variability for fMRI studies in the spinal cord. There is a need for more dialogue within the community on the HRF confound, and we hope that our article is a catalyst in the process