Improved detection of time windows of brain responses in fMRI using modified temporal clustering analysis

Temporal clustering analysis (TCA) has been proposed recently as a method to detect time windows of brain responses in functional MRI (fMRI) studies when the timing and location of the activation are completely unknown. Modifications to the TCA technique are introduced in this report to further improve the sensitivity in detecting brain activation. The modified TCA is based on the integrated signal intensity of a temporal cluster at each time point, while the original TCA is based only on the size of a temporal cluster at each time point. A temporal cluster at each time point is defined, in both TCA methods, as a group of pixels reaching their maximum (or minimum) values at the same time. Both computer simulation and in vivo fMRI experiments have been performed. Compared with the original TCA, the modified TCA shows a significant improvement in the sensitivity to detect activation peaks for determining time windows of brain responses.     

An improved temporal clustering analysis method applied to whole-brain data in fMRI study

Temporal clustering analysis (TCA) has been proposed as a method to detect the brain responses of an fMRI time series when the time and location of the activation are completely unknown. But TCA is still incompetent in dealing with the time series of the whole brain due to the existence of many inactive pixels. If only active pixels are considered, the sensitivity of TCA will be improved greatly and it could be applied to the whole brain. In this study, some modifications were made to TCA to remove inactive pixels, and the applicability of the modified TCA to the whole brain was validated with a set of visual fMRI data. Based on the time series of the modified TCA, activations of the whole brain corresponding to the visual stimulation were detected. Compared with the previous TCA, the modified TCA method shows a significant improvement in the sensitivity to detect activation peaks of the whole brain.     

Improved temporal clustering analysis method applied to whole-brain data in acupuncture fMRI study

Temporal clustering analysis (TCA) has been proposed as a method for detecting the brain responses of a functional magnetic resonance imaging (fMRI) time series when the time and location of activation are completely unknown. But TCA is not suitable for treating the time series of the whole brain due to the existence of many inactive pixels. In theory, active pixels are located only in gray matter (GM). In this study, SPM2 was used to segment functional images into GM, white matter and cerebrospinal fluid, and only the pixels in GM were considered. Thus, most of inactive pixels are deleted, so that the sensitivity of TCA is greatly improved in the analysis of the whole brain. The same set of acupuncture fMRI data was treated using both conventional TCA and modified TCA (MTCA) for comparing their analytical ability. The results clearly show a significant improvement in the sensitivity achieved by MTCA.     

Statistical analysis of the temporal single-photon response of superconducting nanowire single photon detection

A new method to study the transient detection efficiency(DE) and pulse amplitude of superconducting nanowire single photon detectors(SNSPD) during the current recovery process is proposed — statistically analyzing the single photon response under photon illumination with a high repetition rate.The transient DE results match well with the DEs deduced from the static current dependence of DE combined with the waveform of a single-photon detection event.This proves that static measurement results can be used to analyze the transient current recovery process after a detection event.The results are relevant for understanding the current recovery process of SNSPDs after a detection event and for determining the counting rate of SNSPDs.     

Controlling the false positive rate in fuzzy clustering using randomization: application to fMRI activation detection

Despite its potential advantages for fMRI analysis, fuzzy C-means (FCM) clustering suffers from limitations such as the need for a priori knowledge of the number of clusters, and unknown statistical significance and instability of the results. We propose a randomization-based method to control the false-positive rate and estimate statistical significance of the FCM results. Using this novel approach, we develop an fMRI activation detection method. The ability of the method in controlling the false-positive rate is shown by analysis of false positives in activation maps of resting-state fMRI data. Controlling the false-positive rate in FCM allows comparison of different fuzzy clustering methods, using different feature spaces, to other fMRI detection methods. In this article, using simulation and real fMRI data, we compare a novel feature space that takes the variability of the hemodynamic response function into account (HRF-based feature space) to the conventional cross-correlation analysis and FCM using the cross-correlation feature space. In both cases, the HRF-based feature space provides a greater sensitivity compared to the cross-correlation feature space and conventional cross-correlation analysis. Application of the proposed method to finger-tapping fMRI data, using HRF-based feature space, detected activation in sub-cortical regions, whereas both of the FCM with cross-correlation feature space and the conventional cross-correlation method failed to detect them.     

Correlation between temporal response of fMRI and fast reaction time in a language task

Correlation between behavioral parameters and fMRI responses can provide an advanced understanding of the neuronal processes. A lexical decision task was employed to examine the correlation between the reaction time (RT) and the temporal parameters in event-related BOLD responses. Word frequency was manipulated in the experiment. RTs for high-frequency, low-frequency and pseudowords were measured during fMRI (417 +/- 9 ms, 631 +/- 22 ms and 658 +/- 15 ms, respectively). For high-frequency words, RTs were significantly shorter than that for low-frequency and pseudowords (p < 0.0005). In the left inferior frontal region, the FWHM of the fMRI responses was significantly correlated with RT (p < 0.001), which may correspond to areas with sustained activation during the whole processing.     

Comparison of two exploratory data analysis methods for fMRI: fuzzy clustering vs. principal component analysis

Exploratory data-driven methods such as Fuzzy clustering analysis (FCA) and Principal component analysis (PCA) may be considered as hypothesis-generating procedures that are complementary to the hypothesis-led statistical inferential methods in functional magnetic resonance imaging (fMRI). Here, a comparison between FCA and PCA is presented in a systematic fMRI study, with MR data acquired under the null condition, i.e., no activation, with different noise contributions and simulated, varying "activation." The contrast-to-noise (CNR) ratio ranged between 1-10. We found that if fMRI data are corrupted by scanner noise only, FCA and PCA show comparable performance. In the presence of other sources of signal variation (e.g., physiological noise), FCA outperforms PCA in the entire CNR range of interest in fMRI, particularly for low CNR values. The comparison method that we introduced may be used to assess other exploratory approaches such as independent component analysis or neural network-based techniques.     

Derivative temporal clustering analysis: detecting prolonged neuronal activity

Temporal clustering analysis (TCA) and independent component analysis (ICA) are promising data-driven techniques in functional magnetic resonance imaging (fMRI) experiments to obtain brain activation maps in conditions with unknown temporal information regarding the neuronal activity. Although comparable to ICA in detecting transient neuronal activities, TCA fails to detect prolonged plateau brain activations. To eliminate this pitfall, a novel derivative TCA (DTCA) method was introduced and its algorithms with different subtraction intervals were tested on simulated data with a pattern of prolonged plateau brain activation. It was found that the best performance of DTCA method in generating functional maps could be obtained if the subtraction interval is equal to or larger than the length of the rising time of the fMRI response. The DTCA method and its theoretical predication were further investigated and validated using in vivo fMRI data sets. By removing the limitations in the previous TCA, DTCA has shown its powerful capability in detecting prolonged plateau neuronal activities.     

A novel approach for fMRI data analysis based on the combination of sparse approximation and affinity propagation clustering

Clustering analysis has been widely used to detect the functional connectivity from functional magnetic resonance imaging (fMRI) data. However, it has some limitations such as enormous computer memory requirement, and difficulty in estimating the number of clusters. In this study, in order to effectually resolve the deficiencies mentioned above, we have proposed a novel approach (SAAPC) for fMRI data analysis, which combines sparsity, an effective assumption for analyzing fMRI signal, with affinity propagation clustering (APC).     

无源声呐多目标检测中反波束成形递推算法及其应用

随着声呐检测能力的提高,多目标干扰下微弱信号的检测问题日益突出。当声呐方位历程显示上出现多个干扰轨迹时,弱目标的检测显得十分困难。自适应噪声抵消(Adaptive Noise Canceling,ANC)技术为抑制多个干扰提供了理论基础,但是求解稳态最佳滤波矩阵存在着技术实现上的困难。
本文提出用一种反波束成形(Inverse Beamforming,IBF)递推算法,在阵元域逐一抵消多个强干扰,从而增强并提取出微弱目标信号。文中给出了递推求解由逆矩阵所表达的最佳滤波矢量的理论推导和相应的公式。利用IBF算法处理海试数据得到了较好的结果,显著改善了强干扰下对微弱信号的检测,甚至在普通波束成形(CBF)中未能显示出来的信号都可以被检测出来。     

Iterative inverse beamforming algorithm and its application in multiple targets detection of passive sonar

With the increasing of detection ability of passive sonar,the weak signal detection problem in multiple interferences becomes more and more important.In the time/bearing record(TBR) display of sonar detection,when there exist traces of multiple interferences,the identification of weak signal is difficult or impossible.The adaptive noise cancellation technique provides the theoretical basis for suppressing strong interferences.But the solution for finding the steady-state optimum filter matrix is quite difficult due to the real time calculation of inverse matrix of input data correlation matrix.The iterative inverse beamforming(IBF) algorithm for solving the optimum filter vector,which is expressed by inverse matrix of the ocean environment data,is derived in this paper,by which,the optimum filter can be eventually expressed as a sum of series simple matrices of constructed from sensor data.Based on the algorithm proposed in this paper,some examples of at sea experiment are provided.The strong interferences are cancelled and the weak signal is emerged,even it didn't appear in the conventional beamforming(CBF) processing.     

Hierarchical clustering to measure connectivity in fMRI resting-state data

Low frequency oscillations, which are temporally correlated in functionally related brain regions, characterize the mammalian brain, even when no explicit cognitive tasks are performed. Functional connectivity MR imaging is used to map regions of the resting brain showing synchronous, regional and slow fluctuations in cerebral blood flow and oxygenation. In this study, we use a hierarchical clustering method to detect similarities of low-frequency fluctuations. We describe one measure of correlations in the low frequency range for classification of resting-state fMRI data. Furthermore, we investigate the contribution of motion and hardware instabilities to resting-state correlations and provide a method to reduce artifacts. For all cortical regions studied and clusters obtained, we quantify the degree of contamination of functional connectivity maps by the respiratory and cardiac cycle. Results indicate that patterns of functional connectivity can be obtained with hierarchical clustering that resemble known neuronal connections. The corresponding voxel time series do not show significant correlations in the respiratory or cardiac frequency band.     

Influence of the temporal response of the detection system on time-resolved laser-induced incandescence signal evolutions

Time-resolved LII (TIRE-LII) measurements are performed simultaneously at two different wavelengths in a sooting, premixed, flat acetylene flame under atmospheric pressure conditions. The influence of temporal response of the detection system on the measured evolution of the LII signal is discussed. The effect of the temporal response on the determination of particle size distributions is quantified for data evaluation starting some nanoseconds after the maximum particle ensemble temperature. Furthermore, it is investigated how the temporal response of a slow detection system affects the determination of accommodation parameters, e.g. thermal accommodation coefficients, and evaporation coefficients, if TIRE-LII signals are modelled including particle heating as well as particle cooling, and if deconvolution techniques are not applied to the measured LII signal. PACS 85.60.Gz     

A signal subspace approach for modeling the hemodynamic response function in fMRI

Many fMRI analysis methods use a model for the hemodynamic response function (HRF). Common models of the HRF, such as the Gaussian or Gamma functions, have parameters that are usually selected a priori by the data analyst. A new method is presented that characterizes the HRF over a wide range of parameters via three basis signals derived using principal component analysis (PCA). Covering the HRF variability, these three basis signals together with the stimulation pattern define signal subspaces which are applicable to both linear and nonlinear modeling and identification of the HRF and for various activation detection strategies. Analysis of simulated fMRI data using the proposed signal subspace showed increased detection sensitivity compared to the case of using a previously proposed trigonometric subspace. The methodology was also applied to activation detection in both event-related and block design experimental fMRI data using both linear and nonlinear modeling of the HRF. The activated regions were consistent with previous studies, indicating the ability of the proposed approach in detecting brain activation without a priori assumptions about the shape parameters of the HRF. The utility of the proposed basis functions in identifying the HRF is demonstrated by estimating the HRF in different activated regions.     

Dissecting cognitive stages with time-resolved fMRI data: a comparison of fuzzy clustering and independent component analysis

In combination with cognitive tasks entailing sequences of sensory and cognitive processes, event-related acquisition schemes allow using functional MRI to examine not only the topography but also the temporal sequence of cortical activation across brain regions (time-resolved fMRI). In this study, we compared two data-driven methods--fuzzy clustering method (FCM) and independent component analysis (ICA)--in the context of time-resolved fMRI data collected during the performance of a newly devised visual imagery task. We analyzed a multisubject fMRI data set using both methods and compared their results in terms of within- and between-subject consistency and spatial and temporal correspondence of obtained maps and time courses. Both FCM and spatial ICA allowed discriminating the contribution of distinct networks of brain regions to the main cognitive stages of the task (auditory perception, mental imagery and behavioural response), with good agreement across methods. Whereas ICA worked optimally on the original time series, averaging with respect to the task onset (and thus introducing some a priori information on the stimulation protocol) was found to be indispensable in the case of FCM. On averaged time series, FCM led to a richer decomposition of the spatio-temporal patterns of activation and allowed a finer separation of the neurocognitive processes subserving the mental imagery task. This study confirms the efficacy of the two examined methods in the data-driven estimation of hemodynamic responses in time-resolved fMRI studies and provides empirical guidelines to their use.     

Semi-supervised clustering algorithm for community structure detection in complex networks

Discovering a community structure is fundamental for uncovering the links between structure and function in complex networks. In this paper, we discuss an equivalence of the objective functions of the symmetric nonnegative matrix factorization (SNMF) and the maximum optimization of modularity density. Based on this equivalence, we develop a new algorithm, named the so-called SNMF-SS, by combining SNMF and a semi-supervised clustering approach. Previous NMF-based algorithms often suffer from the restriction of measuring network topology from only one perspective, but our algorithm uses a semi-supervised mechanism to get rid of the restriction. The algorithm is illustrated and compared with spectral clustering and NMF by using artificial examples and other classic real world networks. Experimental results show the significance of the proposed approach, particularly, in the cases when community structure is obscure.     

Combined clustering models for the analysis of gene expression

Clustering has become one of the fundamental tools for analyzing gene expression and producing gene classifications. Clustering models enable finding patterns of similarity in order to understand gene function, gene regulation, cellular processes and sub-types of cells. The clustering results however have to be combined with sequence data or knowledge about gene functionality in order to make biologically meaningful conclusions. In this work, we explore a new model that integrates gene expression with sequence or text information.     

A quantitative comparison of motion detection algorithms in fMRI

An important step in the analysis of fMRI time-series data is to detect, and as much as possible, correct for subject motion during the course of the scanning session. Several public domain algorithms are currently available for motion detection in fMRI. This paper compares the performance of four commonly used programs: AIR 3.08, SPM99, AFNI98, and the pyramid method of Thévenaz, Ruttimann, and Unser (TRU). The comparison is based on the performance of the algorithms in correcting a range of simulated known motions in the presence of various degrees of noise. SPM99 provided the most accurate motion detection amongst the algorithms studied. AFNI98 provided only slightly less accurate results than SPM99, however, it was several times faster than the other programs. This algorithm represents a good compromise between speed and accuracy. AFNI98 was also the most robust program in presence of noise. It yielded reasonable results for very low signal to noise levels. For small initial misalignments, TRU's performance was similar to SPM99 and AFNI98. However, its accuracy diminished rapidly for larger misalignments. AIR was found to be the least accurate program studied.     

Long-term clustering, scaling, and universality in the temporal occurrence of earthquakes

Analyzing diverse seismic catalogs, we have determined that the probability densities of the earthquake recurrence times for different spatial areas and magnitude ranges can be described by a unique universal distribution if the time is rescaled with the rate of seismic occurrence, which therefore fully governs seismicity. The shape of the distribution shows the existence of clustering beyond the duration of aftershock bursts, and scaling reveals the self-similarity of the clustering structure in the space-time-magnitude domain. This holds from worldwide to local scales, for quite different tectonic environments and for all the magnitude ranges considered.