Investigating the neural basis for fMRI-based functional connectivity in a blocked design: application to interregional correlations and psycho-physiological interactions

This paper investigates how well different kinds of fMRI functional connectivity analysis reflect the underlying interregional neural interactions. This is hard to evaluate using real experimental data where such relationships are unknown. Rather, we use a biologically realistic neural model to simulate both neuronal activities and multiregional fMRI data from a blocked design. Because we know how every element in the model is related to every other element, we can compare functional connectivity measurements across different spatial and temporal scales. We focus on (1) psycho-physiological interaction (PPI) analysis, which is a simple brain connectivity method that characterizes the activity in one brain region by the interaction between another region's activity and a psychological factor, and (2) interregional correlation analysis. We investigated the neurobiological underpinnings of PPI using simulated neural activities and fMRI signals generated by a large-scale neural model that performs a visual delayed match-to-sample task. Simulated fMRI data are generated by convolving integrated synaptic activities (ISAs) with a hemodynamic response function. The simulation was done under three task conditions: high-attention, low-attention and a control task ('passive viewing'). We investigated how biological and scanning parameters affect PPI and compared these with functional connectivity measures obtained using correlation analysis. We performed correlational and PPI analyses with three types of time-series data: ISA, fMRI and deconvolved fMRI (which yields estimated neural signals) obtained using a deconvolution algorithm. The simulated ISA can be considered as the 'gold standard' because it represents the underlying neural activity. Our main findings show (1) that evaluating the change in an interregional functional connection using the difference in regression coefficients (as is essentially done in the PPI method) produces results that better reflect the underlying changes in neural interrelationships than does evaluating the functional connectivity difference as a change in correlation coefficient; (2) that using fMRI and deconvolved fMRI data led to similar conclusions in the PPI-based functional connectivity results, and these generally agreed with the nature of the underlying neural interactions; and (3) the functional connectivity correlation measures often led to different conclusions regarding significance for different scanning and hemodynamic parameters, but the significances of the PPI regression parameters were relatively robust. These results highlight the way in which neural modeling can be used to help validate the inferences one can make about functional connectivity based on fMRI data.     

Estimation of the effective and functional human cortical connectivity with structural equation modeling and directed transfer function applied to high-resolution EEG

Different brain imaging devices are presently available to provide images of the human functional cortical activity, based on hemodynamic, metabolic or electromagnetic measurements. However, static images of brain regions activated during particular tasks do not convey the information of how these regions are interconnected. The concept of brain connectivity plays a central role in the neuroscience, and different definitions of connectivity, functional and effective, have been adopted in literature. While the functional connectivity is defined as the temporal coherence among the activities of different brain areas, the effective connectivity is defined as the simplest brain circuit that would produce the same temporal relationship as observed experimentally among cortical sites. The structural equation modeling (SEM) is the most used method to estimate effective connectivity in neuroscience, and its typical application is on data related to brain hemodynamic behavior tested by functional magnetic resonance imaging (fMRI), whereas the directed transfer function (DTF) method is a frequency-domain approach based on both a multivariate autoregressive (MVAR) modeling of time series and on the concept of Granger causality.

This study presents advanced methods for the estimation of cortical connectivity by applying SEM and DTF on the cortical signals estimated from high-resolution electroencephalography (EEG) recordings, since these signals exhibit a higher spatial resolution than conventional cerebral electromagnetic measures. To estimate correctly the cortical signals, we used a subject's multicompartment head model (scalp, skull, dura mater, cortex) constructed from individual MRI, a distributed source model and a regularized linear inverse source estimates of cortical current density. Before the application of SEM and DTF methodology to the cortical waveforms estimated from high-resolution EEG data, we performed a simulation study, in which different main factors (signal-to-noise ratio, SNR, and simulated cortical activity duration, LENGTH) were systematically manipulated in the generation of test signals, and the errors in the estimated connectivity were evaluated by the analysis of variance (ANOVA). The statistical analysis returned that during simulations, both SEM and DTF estimators were able to correctly estimate the imposed connectivity patterns under reasonable operative conditions, that is, when data exhibit an SNR of at least 3 and a LENGTH of at least 75 s of nonconsecutive EEG recordings at 64 Hz of sampling rate.

Hence, effective and functional connectivity patterns of cortical activity can be effectively estimated under general conditions met in any practical EEG recordings, by combining high-resolution EEG techniques and linear inverse estimation with SEM or DTF methods. We conclude that the estimation of cortical connectivity can be performed not only with hemodynamic measurements, but also with EEG signals treated with advanced computational techniques.     

Non-linear filtering of ultrasonic signals using neural networks

Structure noise from inhomogeneous micro-structures makes the detection of flaws present in highly scattering materials difficult. Several techniques have been applied to improve the signal-to-noise ratio (SNR) in order to make flaw detection easier. Linear filtering does not provide good results because both structure noise and flaw signal concentrate energy in the same frequency band. Non-linear filtering can be used to reduce the structure noise of ultrasonic signals. Therefore, neural networks are applied in this work for this purpose. In order to use neural networks for non-linear filtering, dynamic structures must be applied. The easiest way to implement a neural network with the capability of processing temporal patterns is to consider them spatial ones, applying the signal into a tapped delay line of finite extension, that is the input of a static neural network (for example, a multi-layer perceptron). In this work, a dynamic neural network has been built to filter ultrasonic signals with structure noise, and has been trained with the real-time back-propagation algorithm, using as inputs 3000 synthetic ultrasonic signals of 896 samples each. Target signals for training are the same as the ones used as inputs but without noise. The neural network is trained in order to generate as output the target signal when the noisy input one is applied. For testing the performance of the non-linear filter, a new set of 500 noisy signals has been used. The SNR improvement is about 6 dB average. The results show that this non-linear filtering method is quite useful as pre-processing stage in flaw detection systems.     

On the use of information theory for the analysis of the relationship between neural and imaging signals

Functional magnetic resonance imaging (fMRI) is a widely used method for studying the neural basis of cognition and of sensory function. A potential problem in the interpretation of fMRI data is that fMRI measures neural activity only indirectly, as a local change of deoxyhemoglobin concentration due to the metabolic demands of neural function. To build correct sensory and cognitive maps in the human brain, it is thus crucial to understand whether fMRI and neural activity convey the same type of information about external correlates. While a substantial experimental effort has been devoted to the simultaneous recordings of hemodynamic and neural signals, so far, the development of analysis methods that elucidate how neural and hemodynamic signals represent sensory information has received less attention. In this article, we critically review why the analytical framework of information theory, the mathematical theory of communication, is ideally suited to this purpose. We review the principles of information theory and explain how they could be applied to the analysis of fMRI and neural signals. We show that a critical advantage of information theory over more traditional analysis paradigms commonly used in the fMRI literature is that it can elucidate, within a single framework, whether an empirically observed correlation between neural and fMRI signals reflects either a similar stimulus tuning or a common source of variability unrelated to the external stimuli. In addition, information theory determines the extent to which these shared sources of stimulus signal and of variability lead fMRI and neural signals to convey similar information about external correlates. We then illustrate the formalism by applying it to the analysis of the information carried by different bands of the local field potential. We conclude by discussing the current methodological challenges that need to be addressed to make the information-theoretic approach more robustly applicable to the simultaneous recordings of neural and imaging data.     

Neural specificity of acupuncture stimulation from support vector machine classification analysis

Acupoint specificity, as a crucial issue in acupuncture neuroimaging studies, is still a controversial topic. Previous studies have generally adopted a block-based general linear model (GLM) approach, which predicts the temporal changes in the blood oxygenation level-dependent signal conforming to the “on-off” specifications. However, this method might become impractical since the precise timing and duration of acupuncture actions cannot be specified a priori. In the current study, we applied a data-driven multivariate classification approach, namely, support vector machine (SVM), to explore the neural specificity of acupuncture at gall bladder 40 (GB40) using kidney 3 (KI3) as a control condition (belonging to different meridians but the same nerve segment). In addition, to verify whether the typical GLM approach is sensitive enough in exploring the neural response patterns evoked by acupuncture, we also employed the GLM method to the same data sets. The SVM analysis detected distinct neural response patterns between GB40 and KI3 — positive predominantly for the GB40, while negative following the KI3. By contrast, group analysis from the GLM showed that acupuncture at these different acupoints can both evoke similar widespread signal decreases in multiple brain regions, and most of these regions were spatially overlapped, mainly distributing in the limbic and subcortical structures. Our findings may provide additional evidence to support the specificity of acupuncture, relevant to its clinical efficacy. Moreover, we also proved that GLM analysis is prone to be susceptible to errors and is not appropriate for detecting neural response patterns evoked by acupuncture stimulation.     

Construction and Application of Functional Brain Network Based on Entropy

Functional brain network (FBN) is an intuitive expression of the dynamic neural activity interaction between different neurons, neuron clusters, or cerebral cortex regions. It can characterize the brain network topology and dynamic properties. The method of building an FBN to characterize the features of the brain network accurately and effectively is a challenging subject. Entropy can effectively describe the complexity, non-linearity, and uncertainty of electroencephalogram (EEG) signals. As a relatively new research direction, the research of the FBN construction method based on EEG data of fatigue driving has broad prospects. Therefore, it is of great significance to study the entropy-based FBN construction. We focus on selecting appropriate entropy features to characterize EEG signals and construct an FBN. On the real data set of fatigue driving, FBN models based on different entropies are constructed to identify the state of fatigue driving. Through analyzing network measurement indicators, the experiment shows that the FBN model based on fuzzy entropy can achieve excellent classification recognition rate and good classification stability. In addition, when compared with the other model based on the same data set, our model could obtain a higher accuracy and more stable classification results even if the length of the intercepted EEG signal is different.     

Component structure of event-related fMRI responses in the different neurovascular compartments

In most functional magnetic resonance imaging (fMRI) studies, brain activity is localized by observing changes in the blood oxygenation level-dependent (BOLD) signal that are believed to arise from capillaries, venules and veins in and around the active neuronal population. However, the contribution from veins can be relatively far downstream from active neurons, thereby limiting the ability of BOLD imaging methods to precisely pinpoint neural generators. Hemodynamic measures based on apparent diffusion coefficients (ADCs) have recently been used to identify more upstream functional blood flow changes in the capillaries, arterioles and arteries. In particular, we recently showed that, due to the complementary vascular sensitivities of ADC and BOLD signals, the voxels conjointly activated by both measures may identify the capillary networks of the active neuronal areas. In this study, we first used simultaneously acquired ADC and BOLD functional imaging signals to identify brain voxels activated by ADC only, by both ADC and BOLD and by BOLD only, thereby delineating voxels relatively dominated by the arterial, capillary, and draining venous neurovascular compartments, respectively. We then examined the event-related fMRI BOLD responses in each of these delineated neurovascular compartments, hypothesizing that their event-related responses would show different temporal componentries. In the regions activated by both the BOLD and ADC contrasts, but not in the BOLD-only areas, we observed an initial transient signal reduction (an initial dip), consistent with the local production of deoxyhemoglobin by the active neuronal population. In addition, the BOLD-ADC overlap areas and the BOLD-only areas showed a clear poststimulus undershoot, whereas the compartment activated by only ADC did not show this component. These results indicate that using ADC contrast in conjunction with BOLD imaging can help delineate the various neurovascular compartments, improve the localization of active neural populations, and provide insight into the physiological mechanisms underlying the hemodynamic signals.     

Activation mapping as a percentage of local excitation: fMRI stability within scans, between scans and across field strengths

Functional magnetic resonance imaging (fMRI) does not typically yield highly reproducible maps of brain activation. Maps can vary significantly even with constant scanning parameters and consistent task performance conditions (Liu et al., Magn. Reson. Med., 2004, 52:751-760). Reproducibility is even more of a problem when comparing fMRI signal magnitude and spatial extent of activation across scans involving different task performance levels, scan durations, pulse sequences or magnetic field strengths. In this report, the consistency of fMRI was reexamined by considering the relative spatial and temporal distribution of fMRI blood oxygen level dependent (BOLD) activation signals separately from the absolute magnitude of the activation signal in each brain area. Subjects repeatedly performed the same simple motor task but under a variety of imaging conditions, using both spiral and standard echo-planar pulse sequences and at 1.5- and 4.0-T magnetic field strengths. The results demonstrate that the absolute amplitude of BOLD statistical activation signals varied significantly across time and scanning conditions, but the relative spatial pattern of BOLD activation was highly reproducible across all conditions. Analysis of realistic simulated fMRI data sets indicates that stability of relative activation patterns could provide a useful tool for assessing the accuracy of fMRI maps.     

Multimodal imaging: an evaluation of univariate and multivariate methods for simultaneous EEG/fMRI

The combination of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) has been proposed as a tool to study brain dynamics with both high temporal and high spatial resolution. Multimodal imaging techniques rely on the assumption of a common neuronal source for the different recorded signals. In order to maximally exploit the combination of these techniques, one needs to understand the coupling (i.e., the relation) between electroencephalographic (EEG) and fMRI blood oxygen level-dependent (BOLD) signals.     

Differences in brain regions of three mice strains identified by label-free micro-Raman

The analysis of different central nervous system regions is interesting and necessary as each one is involved in specific physiological processes and pathologies. On that matter, differences in the chemical composition between the same brain regions in different mice strains have been reported. In this sense, the development of a simple method for the identification of these regions depending on their chemical composition becomes relevant. Raman microspectroscopy, a non-destructive analytical chemical approach for biological samples, is a widely used method for qualitative, quantitative, and structural analysis in biochemical research. Ten brain structures in three different mice strains (Triple transgenic for Alzheimer Disease, 3xTgAD; Cluster 57 black 6, C57BL/6; and the Swiss strain, CD1) were analyzed, and variations among samples from several brain regions were found. Particularly, the pattern of signals from the hippocampus, the prefrontal and temporal cortices, the basal forebrain, the striatum, the cerebellum, and the hypothalamus was discernable. Interestingly, notable signals regarding non-peptide small neurotransmitters were observed, including those related to acetylcholine. These bands were present in the Raman spectra of the basal forebrain and prefrontal cortex in the three mice strains, consistent with the relative abundance of this neurotransmitter in those regions. However, signals with lower intensities appeared in the basal forebrain of C57BL/6 in comparison with the same tissue of the other two strains. In addition, the Raman intensity of bands assigned to catecholamines in the striatum was lower in the 3xTgAD than those from both CD1 and C57BL/6 mice strains. This approach, as well as the reported differences, has potential application for designing analysis on specific murine models of brain diseases.     

Comodulation detection differences with multiple signal bands

Detection thresholds were determined for signals consisting of one, two, or five noise bands embedded in eight "cue" bands. All of the noise bands were 100 Hz wide. The center frequencies of the signal bands ranged from 1250-3250 Hz in 500-Hz steps, and those of the cue bands ranged from 500-4000 Hz in 500-Hz steps. The multiple-band signals either all had the same temporal envelope, or all had different temporal envelopes. Similarly, the cue bands either all had the same temporal envelope or all had different temporal envelopes. In separate listening conditions, signal thresholds were determined for various combinations of the temporal envelope patterns of the signal and cue bands. The results were analyzed both in terms of differences in threshold across listening conditions, and in terms of changes in threshold within a listening condition, as the number of signal bands was increased. For both the single- and multiple-band signals, performance was best when the signal band(s) had a different envelope from the common envelope of the cue bands, and performance was worst when either the cue bands all had different envelopes, or the signal and cue bands all shared the same envelope. The thresholds of the multiple-band signals were better fitted by an independent-thresholds model than by a statistical-summation model. However, neither model predicted thresholds uniformly well in all listening conditions. The results are discussed in terms of both "within-channel" and "across-channel" models.     

自适应分段时域质心特征在鱼类识别中的应用

提出了一种基于时域质心的时域自适应分段方法。该方法以时域质心为依据对信号的时域进行划分,在划分的各个子段内计算时域质心,并将其作为下一层划分的分割点。各个子段内的时域质心反映了信号的能量分布特性,可作为识别特征量。对三种常见的不同形状的鱼类进行了水池试验,提取自适应分段时域质心特征,并使用BP神经网络分类器成功进行了分类。结果表明:利用自适应分段时域质心特征可对不同形状的鱼类进行识别,且具有较高的识别率。     

基于虚拟开车环境的自闭症儿童脑电样本熵

自闭症谱系障碍是一种涉及感觉、情感、记忆、语言、智力、动作等认知功能和执行功能障碍的精神疾病. 本文从神经工效学角度出发, 用虚拟开车环境作为复杂多任务激励源将大脑系统与人体动作控制等有机地结合起来, 通过对脑电信号的滑动平均样本熵分析来探索自闭症儿童在虚拟开车环境中的脑活动特征. 研究发现不论是休息状态还是开车状态, 自闭症患者的滑动平均样本熵总体上低于健康者, 尤其在前额叶、颞叶、顶叶和枕叶功能区, 表明自闭症儿童的行为适应性较低. 不过, 自闭症患者的开车状态与健康受试者的休息状态比较接近, 表明虚拟开车环境或许有助于自闭症患者的干预治疗. 此外, 自闭症患者在颞叶区呈现显著性右半球优势性. 本研究为进一步深入开展自闭症疾病的机理研究及其诊断、评估和干预等研究提供一种新的研究思路.     

To smooth or not to smooth? ROC analysis of perfusion fMRI data

Blood oxygenation level dependent (BOLD) contrast has been widely used for visualizing regional neural activation. Temporal filtering and parameter estimation algorithms are generally used to account for the intrinsic temporal autocorrelation present in BOLD data. Arterial spin labeling perfusion imaging is an emerging methodology for visualizing regional brain function both at rest and during activation. Perfusion contrast manifests different noise properties compared with BOLD contrast, represented by the even distribution of noise power and spatial coherence across the frequency spectrum. Consequently, different strategies are expected to be employed in the statistical analysis of functional magnetic resonance imaging (fMRI) data based on perfusion contrast. In this study, the effect of different analysis methods upon signal detection efficacy, as assessed by receiver operator characteristic (ROC) measures, was examined for perfusion fMRI data. Simulated foci of neural activity of varying amplitude and spatial extent were added to resting perfusion data, and the accuracy of each analysis was evaluated by comparing the results with the known distribution of pseudo-activation. In contrast to the BOLD fMRI, temporal smoothing or filtering reduces the power of perfusion fMRI data analyses whereas spatial smoothing is beneficial to the efficacy of analyses.     

Oscillatory activity in excitable neural systems

The brain is a complex system and exhibits various subsystems on different spatial and temporal scales. These subsystems are recurrent networks of neurons or populations that interact with each other. The single neurons are microscopic objects and evolve on a different time scale than macroscopic neural populations. To understand the dynamics of the brain, however, it is necessary to understand the dynamics of the brain network both on the microscopic and the macroscopic level and the interaction between the levels. The presented work introduces one to the major properties of single neurons and their interactions. The physical aspects of some standard mathematical models are discussed in some detail. The work shows that both single neurons and neural populations are excitable in the sense that small differences in an initial short stimulation may yield very different dynamical behaviour of the system. To illustrate the power of the neural population model discussed, the work applies the model to explain experimental activity in the delayed feedback system in weakly electric fish and the electroencephalogram (EEG).     

Field strength influences on gradient recalled echo MRI signal compartment frequency shifts

Different trends of echo time dependent gradient recalled echo MRI signals in different brain regions have been attributed to signal compartments in image voxels. It remains unclear how variations in gradient recalled echo MRI signals change as a function of MRI field strength, and how data processing may impact signal compartment parameters. We used two popular quantitative susceptibility mapping methods of processing raw phase images (Laplacian and path-based unwrapping with V-SHARP) and expressed values in the form of induced frequency shifts (in Hz) in six specific brain regions at 3T and 7T. We found the frequency shift curves to vary with echo time, and a good overlap between 3T and 7T mean frequency shift curves was present. However, the amount of variation across participants was greater at 3T, and we were able to obtain better compartment model fits of the signal at 7T. We also found the temporal trends in the signal and compartment frequency shifts to change with the method used to process images. The inter-participant averaged trends were consistent between 3T and 7T for each quantitative susceptibility pipeline. However, signal compartment frequency shifts generated using different pipelines may not be comparable.     

Percept-related activity in the human somatosensory system: functional magnetic resonance imaging studies

In this paper, we review blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) studies addressing the neural correlates of touch, thermosensation, pain and the mechanisms of their cognitive modulation in healthy human subjects. There is evidence that fMRI signal changes can be elicited in the parietal cortex by stimulation of single mechanoceptive afferent fibers at suprathreshold intensities for conscious perception. Positive linear relationships between the amplitude or the spatial extents of BOLD fMRI signal changes, stimulus intensity and the perceived touch or pain intensity have been described in different brain areas. Some recent fMRI studies addressed the role of cortical areas in somatosensory perception by comparing the time course of cortical activity evoked by different kinds of stimuli with the temporal features of touch, heat or pain perception. Moreover, parametric single-trial functional MRI designs have been adopted in order to disentangle subprocesses within the nociceptive system.

Available evidence suggest that studies that combine fMRI with psychophysical methods may provide a valuable approach for understanding complex perceptual mechanisms and top-down modulation of the somatosensory system by cognitive factors specifically related to selective attention and to anticipation. The brain networks underlying somatosensory perception are complex and highly distributed. A deeper understanding of perceptual-related brain mechanisms therefore requires new approaches suited to investigate the spatial and temporal dynamics of activation in different brain regions and their functional interaction.     

Arithmetic mismatch negativity and numerical magnitude processing in number matching

Background

After a prolonged exposure to a paired presentation of different types of signals (e.g., color and motion), one of the signals (color) becomes a driver for the other signal (motion). This phenomenon, which is known as contingent motion aftereffect, indicates that the brain can establish new neural representations even in the adult's brain. However, contingent motion aftereffect has been reported only in visual or auditory domain. Here, we demonstrate that a visual motion aftereffect can be contingent on a specific sound.

Results

Dynamic random dots moving in an alternating right or left direction were presented to the participants. Each direction of motion was accompanied by an auditory tone of a unique and specific frequency. After a 3-minutes exposure, the tones began to exert marked influence on the visual motion perception, and the percentage of dots required to trigger motion perception systematically changed depending on the tones. Furthermore, this effect lasted for at least 2 days.

Conclusions

These results indicate that a new neural representation can be rapidly established between auditory and visual modalities.     

Sound segregation based on temporal envelope structure and binaural cues

The ability to segregate two spectrally and temporally overlapping signals based on differences in temporal envelope structure and binaural cues was investigated. Signals were a harmonic tone complex (HTC) with 20 Hz fundamental frequency and a bandpass noise (BPN). Both signals had interaural differences of the same absolute value, but with opposite signs to establish lateralization to different sides of the medial plane, such that their combination yielded two different spatial configurations. As an indication for segregation ability, threshold interaural time and level differences were measured for discrimination between these spatial configurations. Discrimination based on interaural level differences was good, although absolute thresholds depended on signal bandwidth and center frequency. Discrimination based on interaural time differences required the signals' temporal envelope structures to be sufficiently different. Long-term interaural cross-correlation patterns or long-term averaged patterns after equalization-cancellation of the combined signals did not provide information for the discrimination. The binaural system must, therefore, have been capable of processing changes in interaural time differences within the period of the harmonic tone complex, suggesting that monaural information from the temporal envelopes influences the use of binaural information in the perceptual organization of signal components.     

Integration of fMRI, NIROT and ERP for studies of human brain function

Different methods of assessing human brain function possess specific advantages and disadvantages compared to others, but it is believed that combining different approaches will provide greater information than can be obtained from each alone. For example, functional magnetic resonance imaging (fMRI) has good spatial resolution but poor temporal resolution, whereas the converse is true for electrophysiological recordings (event-related potentials or ERPs). In this review of recent work, we highlight a novel approach to combining these modalities in a manner designed to increase information on the origins and locations of the generators of specific ERPs and the relationship between fMRI and ERP signals. Near infrared imaging techniques have also been studied as alternatives to fMRI and can be readily integrated with simultaneous electrophysiological recordings. Each of these modalities may in principle be also used in so-called steady-state acquisitions in which the correlational structure of signals from the brain may be analyzed to provide new insights into brain function.