A kernel machine-based fMRI physiological noise removal method

Functional magnetic resonance imaging (fMRI) technique with blood oxygenation level dependent (BOLD) contrast is a powerful tool for noninvasive mapping of brain function under task and resting states. The removal of cardiac- and respiration-induced physiological noise in fMRI data has been a significant challenge as fMRI studies seek to achieve higher spatial resolutions and characterize more subtle neuronal changes. The low temporal sampling rate of most multi-slice fMRI experiments often causes aliasing of physiological noise into the frequency range of BOLD activation signal. In addition, changes of heartbeat and respiration patterns also generate physiological fluctuations that have similar frequencies with BOLD activation. Most existing physiological noise-removal methods either place restrictive limitations on image acquisition or utilize filtering or regression based post-processing algorithms, which cannot distinguish the frequency-overlapping BOLD activation and the physiological noise. In this work, we address the challenge of physiological noise removal via the kernel machine technique, where a nonlinear kernel machine technique, kernel principal component analysis, is used with a specifically identified kernel function to differentiate BOLD signal from the physiological noise of the frequency. The proposed method was evaluated in human fMRI data acquired from multiple task-related and resting state fMRI experiments. A comparison study was also performed with an existing adaptive filtering method. The results indicate that the proposed method can effectively identify and reduce the physiological noise in fMRI data. The comparison study shows that the proposed method can provide comparable or better noise removal performance than the adaptive filtering approach.     

Deconvolution filtering: Temporal smoothing revisited

Inferences made from analysis of BOLD data regarding neural processes are potentially confounded by multiple competing sources: cardiac and respiratory signals, thermal effects, scanner drift, and motion-induced signal intensity changes. To address this problem, we propose deconvolution filtering, a process of systematically deconvolving and reconvolving the BOLD signal via the hemodynamic response function such that the resultant signal is composed of maximally likely neural and neurovascular signals. To test the validity of this approach, we compared the accuracy of BOLD signal variants (i.e., unfiltered, deconvolution filtered, band-pass filtered, and optimized band-pass filtered BOLD signals) in identifying useful properties of highly confounded, simulated BOLD data: (1) reconstructing the true, unconfounded BOLD signal, (2) correlation with the true, unconfounded BOLD signal, and (3) reconstructing the true functional connectivity of a three-node neural system. We also tested this approach by detecting task activation in BOLD data recorded from healthy adolescent girls (control) during an emotion processing task.     

Comparison of α-chloralose,medetomidine and isoflurane anesthesia for functional connectivity mapping in the rat

Functional connectivity measures based upon low-frequency blood-oxygenation-level-dependent functional magnetic resonance imaging (BOLD fMRI) signal fluctuations have become a widely used tool for investigating spontaneous brain activity in humans. Still unknown, however, is the precise relationship between neural activity, the hemodynamic response and fluctuations in the MRI signal. Recent work from several groups had shown that correlated low-frequency fluctuations in the BOLD signal can be detected in the anesthetized rat — a first step toward elucidating this relationship. Building on this preliminary work, through this study, we demonstrate that functional connectivity observed in the rat depends strongly on the type of anesthesia used. Power spectra of spontaneous fluctuations and the cross-correlation-based connectivity maps from rats anesthetized with α-chloralose, medetomidine or isoflurane are presented using a high-temporal-resolution imaging sequence that ensures minimal contamination from physiological noise. The results show less localized correlation in rats anesthetized with isoflurane as compared with rats anesthetized with α-chloralose or medetomidine. These experiments highlight the utility of using different types of anesthesia to explore the fundamental physiological relationships of the BOLD signal and suggest that the mechanisms contributing to functional connectivity involve a complicated relationship between changes in neural activity, neurovascular coupling and vascular reactivity.     

Relationship between neural and hemodynamic signals during spontaneous activity studied with temporal kernel CCA

Functional magnetic resonance imaging (fMRI) based on the so-called blood oxygen level-dependent (BOLD) contrast is a powerful tool for studying brain function not only locally but also on the large scale. Most studies assume a simple relationship between neural and BOLD activity, in spite of the fact that it is important to elucidate how the “when” and “what” components of neural activity are correlated to the “where” of fMRI data. Here we conducted simultaneous recordings of neural and BOLD signal fluctuations in primary visual (V1) cortex of anesthetized monkeys. We explored the neurovascular relationship during periods of spontaneous activity by using temporal kernel canonical correlation analysis (tkCCA). tkCCA is a multivariate method that can take into account any features in the signals that univariate analysis cannot. The method detects filters in voxel space (for fMRI data) and in frequency–time space (for neural data) that maximize the neurovascular correlation without any assumption of a hemodynamic response function (HRF). Our results showed a positive neurovascular coupling with a lag of 4–5 s and a larger contribution from local field potentials (LFPs) in the γ range than from low-frequency LFPs or spiking activity. The method also detected a higher correlation around the recording site in the concurrent spatial map, even though the pattern covered most of the occipital part of V1. These results are consistent with those of previous studies and represent the first multivariate analysis of intracranial electrophysiology and high-resolution fMRI.     

Testing methodologies for the nonlinear analysis of causal relationships in neurovascular coupling

We investigated the use and implementation of a nonlinear methodology for establishing which changes in neurophysiological signals cause changes in the blood oxygenation level-dependent (BOLD) contrast measured in functional magnetic resonance imaging. Unlike previous analytical approaches, which used linear correlation to establish covariations between neural activity and BOLD, we propose a directed information-theoretic measure, the transfer entropy, which can elucidate even highly nonlinear causal relationships between neural activity and BOLD signal. In this study we investigated the practicality of such an analysis given the limited data samples that can be collected experimentally due to the low temporal resolution of BOLD signals. We implemented several algorithms for the estimation of transfer entropy and we tested their effectiveness using simulated local field potentials (LFPs) and BOLD data constructed to match the main statistical properties of real LFP and BOLD signals measured simultaneously in monkey primary visual cortex. We found that using the advanced methods of entropy estimation implemented and described here, a transfer entropy analysis of neurovascular coupling based on experimentally attainable data sets is feasible.     

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.     

The effects of respiratory CO2 fluctuations in the resting-state BOLD signal differ between eyes open and eyes closed

Resting fluctuations in arterial CO₂ (a cerebral vasodilator) are believed to be an important source of low-frequency blood oxygenation level dependent (BOLD) signal fluctuations. In this study we focus on the two commonly used resting-states in functional magnetic resonance imaging experiments, eyes open and eyes closed, and quantify the degree to which measured spontaneous fluctuations in the partial pressure of end-tidal CO₂ (Pet_co2) relate to BOLD signal time series. A significantly longer latency of BOLD signal changes following Pet_co2 fluctuations was found in the eyes closed condition compared to with eyes open, which may reveal different intrinsic vascular response delays in CO₂ reactivity or an alteration in the net BOLD signal arising from Pet_co2 fluctuations and altered neural activity with eyes closed. By allowing a spatially varying time delay for the compensation of this temporal difference, a more spatially consistent CO₂ correlation map can be obtained. Finally, Granger-causality analysis demonstrated a “causal” relationship between Pet_co2 and BOLD. The identified dominant Pet_co2→BOLD directional coupling supports the notion that Pet_co2 fluctuations are indeed a cause of resting BOLD variance in the majority of subjects.     

Sparsity constrained deconvolution approaches for acoustic source mapping

Using microphone arrays for estimating source locations and strengths has become common practice in aeroacoustic applications. The classical delay-and-sum approach suffers from low resolution and high sidelobes and the resulting beamforming maps are difficult to interpret. The deconvolution approach for the mapping of acoustic sources (DAMAS) deconvolution algorithm recovers the actual source levels from the contaminated delay-and-sum results by defining an inverse problem that can be represented as a linear system of equations. In this paper, the deconvolution problem is carried onto the sparse signal representation area and a sparsity constrained deconvolution approach (SC-DAMAS) is presented for solving the DAMAS inverse problem. A sparsity preserving covariance matrix fitting approach (CMF) is also presented to overcome the drawbacks of the DAMAS inverse problem. The proposed algorithms are convex optimization problems. Our simulations show that CMF and SC-DAMAS outperform DAMAS and as the noise in the measurements increases, CMF works better than both DAMAS and SC-DAMAS. It is observed that the proposed algorithms converge faster than DAMAS. A modification to SC-DAMAS is also provided which makes it significantly faster than DAMAS and CMF. For the correlated source case, the CMF-C algorithm is proposed and compared with DAMAS-C. Improvements in performance are obtained similar to the uncorrelated case.     

Neuronal event detection in fMRI time series using iterative deconvolution techniques

An iterative estimation algorithm for deconvolution of neuronal activity from Blood Oxygen Level Dependent (BOLD) time series data is presented. The algorithm requires knowledge of the hemodynamic impulse response function but does not require knowledge of the stimulation function. The method uses majorization-minimization of a cost function to find an optimal solution to the inverse problem. The cost function includes penalties for the l₁ norm, total variation and negativity. The algorithm is able to identify the occurrence of neuronal activity bursts from BOLD time series accurately. The accuracy of the algorithm was tested in simulations and experimental fMRI data using blocked and event-related designs. The simulations revealed that the algorithm is most sensitive to contrast-to-noise ratio levels and to errors in the assumed hemodynamic model and least sensitive to autocorrelation in the noise. Within normal fMRI conditions, the method is effective for event detection.     

Separation of physiological very low frequency fluctuation from aliasing by switched sampling interval fMRI scans

Anesthetized children have dominant blood-oxygen-level-dependent (BOLD) signal sources presenting high-power fluctuations at very low frequencies (VLF <0.05 Hz). Aliasing of frequencies higher than critically sampled has been regarded as one probable origin of the VLF fluctuations. Aliased signal frequencies change when the sampling rate of the data is altered. In this study, the aliasing of VLF BOLD signal fluctuation was analysed by switching the repetition time (TR) of magnetic resonance (MR) images. Eleven anesthetized children were imaged at 1.5 T using TRs of 500 and 1200 ms. The BOLD signal sources were separated with independent component analysis (ICA). Occipital cortex signal sources had nonaliased VLF fluctuation ( approximately 0.03 Hz) in 9 of 11 subjects. Arterial signal sources failed to present stable power peaks at frequencies lower than 0.42 Hz presumably due to aliasing. Cerebrospinal fluid (CSF)-related signal sources showed nonaliased VLF in four subjects. In conclusion, the VLF BOLD signal fluctuation in the occipital cortex is a true physiological fluctuation, not a result of signal aliasing.     

A new algorithm of active suppression of noise signals in real time measurements

A new algorithm of the suppression of pickup noise and background in information signals in real time measurements is considered. This algorithm is based on a recurrent method of spectral-coefficient measurements of noise component in an analyzed signal and a recursive filtration algorithm for its suppression. Using recurrent calculations in the new algorithm makes it possible to perform a dynamic spectral measurements of information signals in real time, which are not possible to do by classical algorithms of spectral transformations due to time restrictions.     

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.     

分布式光纤中的稳健时间延迟估计方法

在分布式光纤传感系统定位中,传统时延估计算法常由于噪声相关性较强而失效。采用一种削弱相关噪声的改进型广义相关法,并针对系统特点,为进一步改善分布式光纤传感定位的准确度与稳定度,提出了一种先对数据按事件信号进行分帧,再采用卡尔曼滤波器对分帧时延估计结果进行跟踪的时延估计方案。系统仿真实验与实际数据测试结果均表明:提出的时延估计方案能够有效抑制强相关性的噪声,提高时延估计的准确度与稳定度。经大量现场测试,本文的方案能够有效地将时延估计误差稳定地控制在0.2个采样间隔以内,能够满足系统实际定位精度要求。     

基于近似l0范数最小化的NMR波谱稀疏重建算法

在核磁共振（NMR）波谱中,过长的数据采集时间会使很多化学以及分子生物学领域的高分辨率多维谱应用难以实现. 传统的解决办法是使用随机非均匀采样代替奈奎斯特采样,但这样会使谱图质量受损. 压缩传感的出现为此提供了更好的解决办法,合适的压缩传感重建算法可以通过很少的随机非均匀采样将谱图高质量的重建出来. 该文先介绍了一种可用于谱图重建的压缩传感重建算法,名为“平滑l₀范数最小化法”,然后针对该算法对采样噪声鲁棒性较差的缺点进行了改进. 通过将改进后的算法与原算法在一维实数域信号以及NMR波谱信号重建实验中进行对比后表明,改进后的算法对噪声的鲁棒性明显提高,并能获得更好的重建性能.     

互补型自适应滤波器在心磁信号处理中的应用

将心磁信号从干扰噪声中加以提取并有效地消除噪声干扰是心磁信号处理中尤为重要的环节 .从改进算法的角度出发，提出互补型自适应滤波器结构以实现心磁信号的消噪处理.该滤波器针对心磁这类非平稳信号进行设计，有效地解决了常规自适应滤波器应用于心磁信号处理时收敛速度和稳态误差的矛盾.通过仿真实验和心磁实验结果表明，该算法能有效地消除心磁信号的背景噪声和工频干扰噪声.同时该算法也可用于其他非平稳信号的消噪处理. 关键词： 自适应滤波 心磁图 最小均方误差     

A Nonlinear Maximum Correntropy Information Filter for High-Dimensional Neural Decoding

Neural signal decoding is a critical technology in brain machine interface (BMI) to interpret movement intention from multi-neural activity collected from paralyzed patients. As a commonly-used decoding algorithm, the Kalman filter is often applied to derive the movement states from high-dimensional neural firing observation. However, its performance is limited and less effective for noisy nonlinear neural systems with high-dimensional measurements. In this paper, we propose a nonlinear maximum correntropy information filter, aiming at better state estimation in the filtering process for a noisy high-dimensional measurement system. We reconstruct the measurement model between the high-dimensional measurements and low-dimensional states using the neural network, and derive the state estimation using the correntropy criterion to cope with the non-Gaussian noise and eliminate large initial uncertainty. Moreover, analyses of convergence and robustness are given. The effectiveness of the proposed algorithm is evaluated by applying it on multiple segments of neural spiking data from two rats to interpret the movement states when the subjects perform a two-lever discrimination task. Our results demonstrate better and more robust state estimation performance when compared with other filters.     

Neural and vascular variability and the fMRI-BOLD response in normal aging

Neural, vascular and structural variables contributing to the blood oxygen level-dependent (BOLD) signal response variability were investigated in younger and older humans. Twelve younger healthy human subjects (six male and six female; mean age: 24 years; range: 19–27 years) and 12 older healthy subjects (five male and seven female; mean age: 58 years; range: 55–71 years) with no history of head trauma and neurological disease were scanned. Functional magnetic resonance imaging measurements using the BOLD contrast were made when participants performed a motor, cognitive or a breath hold (BH) task. Activation volume and the BOLD response amplitude were estimated for the younger and older at both group and subject levels. Mean activation volume was reduced by 45%, 40% and 38% in the elderly group during the motor, cognitive and BH tasks, respectively, compared to the younger. Reduction in activation volume was substantially higher compared to the reduction in the gray matter volume of 14% in the older compared to the younger. A significantly larger variability in the intersubject BOLD signal change occurred during the motor task, compared to the cognitive task. BH-induced BOLD signal change between subjects was significantly less-variable in the motor task-activated areas in the younger compared to older whereas such a difference between age groups was not observed during the cognitive task. Hemodynamic scaling using the BH signal substantially reduced the BOLD signal variability during the motor task compared to the cognitive task. The results indicate that the origin of the BOLD signal variability between subjects was predominantly vascular during the motor task while being principally a consequence of neural variability during the cognitive task. Thus, in addition to gray matter differences, the type of task performed can have different vascular variability weighting that can influence age-related differences in brain functional response.     

A novel feedback active noise control for broadband chaotic noise and random noise

The feedback active noise control (ANC) can be seen as a predictor, the conventional method based on filtered-x least mean square (FXLMS) algorithm can only be useful for linear and tonal noise, but for nonlinear and broadband noise, it is useless. The feedback ANC using functional link artificial neural networks (FLANN) based on filtered-s least mean square (FSLMS) algorithm can reduce some nonlinear noise such as chaotic noise, but the noise cancellation performance is not very well, at the same time, it is not useful to random noise. To solve the problem above, a new feedback ANC using wavelet packet FXLMS (WPFXLMS) algorithm is proposed in this paper. By decomposing the broadband noise into several band-limited parts which are predictable and each part is controlled independently, the proposed algorithm can not only suppress the chaotic noise, but also mitigate the random noise. Compared with FXLMS and FSLMS algorithms, proposed WPFXLMS algorithm also holds the best performance on noise cancellation. Numerous simulations are conducted to demonstrate the effectiveness of the proposed WPFXLMS algorithm.     

Spontaneous low-frequency blood oxygenation level-dependent fluctuations and functional connectivity analysis of the 'resting' brain

Functional magnetic resonance imaging techniques using the blood oxygenation level-dependent (BOLD) contrast are widely used to map human brain function by relating local hemodynamic responses to neuronal stimuli compared to control conditions. There is increasing interest in spontaneous cerebral BOLD fluctuations that are prominent in the low-frequency range (<0.1 Hz) and show intriguing spatio-temporal correlations in functional networks. The nature of these signal fluctuations remains unclear, but there is accumulating evidence for a neural basis opening exciting new avenues to study human brain function and its connectivity at rest. Moreover, an increasing number of patient studies report disease-dependent variation in the amplitude and spatial coherence of low-frequency BOLD fluctuations (LFBF) that may afford greater diagnostic sensitivity and easier clinical applicability than standard fMRI. The main disadvantage of this emerging tool relates to physiological (respiratory, cardiac and vasomotion) and motion confounds that are challenging to disentangle requiring thorough preprocessing. Technical aspects of functional connectivity fMRI analysis and the neuroscientific potential of spontaneous LFBF in the default mode and other resting-state networks have been recently reviewed. This review will give an update on the current knowledge of the nature of LFBF, their relation to physiological confounds and potential for clinical diagnostic and pharmacological studies.