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1.
Magnetic resonance imaging (MRI) has recently been applied to study spinal cord function in humans. However, spinal functional MRI (fMRI) encounters major technical challenges with cardiac noise being considered a major source of noise. The present study relied on echo-planar imaging of the cervical cord at short TR (TR=250 ms; TE=40 ms; flip=45 degrees), combined with plethysmographic recordings to characterize the spatiotemporal properties of cardiac-induced signal changes in spinal fMRI. Frequency-based analyses examining signal change at the cardiac frequency confirmed mean fluctuations of about 10% (relative to the mean signal) in the spinal cord and surrounding cerebrospinal fluid (CSF), with maximal responses reaching up to 66% in some voxels. A spatial independent component analysis (sICA) confirmed that cardiac noise is an important source of variance in spinal fMRI with several components showing a response coherent with the cardiac frequency spectrum. The time course of the main cardiac components approximated a sinusoidal function tightly coupled to the cardiac systole with at least one component showing a comparable temporal profile across runs and subjects. Spatially, both the frequency-domain analysis and the sICA demonstrated cardiac noise distributed irregularly along the full rostrocaudal extent of the segments scanned with peaks concentrated in the ventral part of the lateral slices in all scans and subjects, consistent with the major channels of CSF flow. These results confirm that cardiac-induced changes are a significant source of noise likely to affect the detection of spinal Blood Oxygen Level Dependent (BOLD) responses. Most importantly, the complex spatiotemporal structure of cardiac noise is unlikely to be accounted for adequately by ad hoc linear methods, especially in data acquired using long TR (i.e. aliasing the cardiac frequency). However, the reliable spatiotemporal distribution of cardiac noise across scanning runs and within subjects may provide a valid means to identify and extract cardiac noise based on sICA methods.  相似文献   

2.
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.  相似文献   

3.
Spatial independent component analysis (ICA) is a well-established technique for multivariate analysis of functional magnetic resonance imaging (fMRI) data. It blindly extracts spatiotemporal patterns of neural activity from functional measurements by seeking for sources that are maximally independent. Additional information on one or more sources (e.g., spatial regularity) is often available; however, it is not considered while looking for independent components. In the present work, we propose a new ICA algorithm based on the optimization of an objective function that accounts for both independence and other information on the sources or on the mixing model in a very general fashion. In particular, we apply this approach to fMRI data analysis and illustrate, by means of simulations, how inclusion of a spatial regularity term helps to recover the sources more effectively than with conventional ICA. The improvement is especially evident in high noise situations. Furthermore we employ the same approach on data sets from a complex mental imagery experiment, showing that consistency and physiological plausibility of relatively weak components are improved.  相似文献   

4.
By measuring the changes of magnetic resonance signals during a stimulation, the functional magnetic resonance imaging (fMRI) is able to localize the neural activation in the brain. In this report, we discuss the fMRI application of the spatial independent component analysis (spatial ICA), which maximizes statistical independence over spatial images. Included simulations show the possibility of the spatial ICA on discriminating asynchronous activations or different response patterns in an fMRI data set. An in vivo visual stimulation fMRI test was conducted, and the result shows a proper sum of the separated components as the final image is better than a single component, using fMRI data analysis by spatial ICA. Our result means that spatial ICA is a useful tool for the detection of different response activations and suggests that a proper sum of the separated independent components should be used for the imaging result of fMRI data processing.  相似文献   

5.
Blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) studies using parallel imaging to reduce the readout window have reported a loss in temporal signal-to-noise ratio (SNR) that is less than would be expected given a purely thermal noise model. In this study, the impact of parallel imaging on the noise components and functional sensitivity of both BOLD and perfusion-based fMRI data was investigated. Dual-echo arterial spin labeling data were acquired on five subjects using sensitivity encoding (SENSE), at reduction factors (R) of 1, 2 and 3. Direct recording of cardiac and respiratory activity during data acquisition enabled the retrospective removal of physiological noise. The temporal SNR of the perfusion time series closely followed the thermal noise prediction of a √R loss in SNR as the readout window was shortened, with temporal SNR values (relative to the R=1 data) of 0.72 and 0.56 for the R=2 and R=3 data, respectively, after accounting for physiological noise. However, the BOLD temporal SNR decreased more slowly than predicted even after accounting for physiological noise, with relative temporal SNR values of 0.80 and 0.63 for the R=2 and R=3 data, respectively. Spectral analysis revealed that the BOLD trends were dominated by low-frequency fluctuations, which were not dominant in the perfusion data due to signal processing differences. The functional sensitivity, assessed using mean F values over activated regions of interest (ROIs), followed the temporal SNR trends for the BOLD data. However, results for the perfusion data were more dependent on the threshold used for ROI selection, most likely due to the inherently low SNR of functional perfusion data.  相似文献   

6.
The quality of fMRI data impacts functional connectivity measures and consequently, the decisions that clinicians and researchers make regarding functional connectivity interpretation. The present study used resting state fMRI to investigate resting state network connectivity in a sample of patients with Juvenile Absence Epilepsy. Single-subject manual independent component analysis was used in two levels, whereby all noise components were removed, and cerebrospinal fluid pulsation components only were isolated and removed. Improved temporal signal to noise ratios and functional connectivity metrics were observed in each of the cleaning levels for both epilepsy and control cohorts. Results showed full, single-subject manual independent component analysis reduced the number of functional connectivity correlations and increased the strength of these correlations. Similar effects were also observed for the cerebrospinal fluid pulsation only cleaned data relative to the uncleaned, and fully cleaned data. Single-subject manual independent component analysis coupled with short TR multiband acquisition can significantly improve the validity of findings derived from fMRI data sets.  相似文献   

7.
Signal fluctuations in functional magnetic resonance imaging (fMRI) can result from a number of sources that may have a neuronal, physiologic or instrumental origin. To determine the relative contribution of these sources, we recorded physiological (respiration and cardiac) signals simultaneously with fMRI in human volunteers at rest with their eyes closed. State-of-the-art technology was used including high magnetic field (7 T), a multichannel detector array and high-resolution (3 mm3) echo-planar imaging. We investigated the relative contribution of thermal noise and other sources of variance to the observed fMRI signal fluctuations both in the visual cortex and in the whole brain gray matter. The following sources of variance were evaluated separately: low-frequency drifts due to scanner instability, effects correlated with respiratory and cardiac cycles, effects due to variability in the respiratory flow rate and cardiac rate, and other sources, tentatively attributed to spontaneous neuronal activity. We found that low-frequency drifts are the most significant source of fMRI signal fluctuations (3.0% signal change in the visual cortex, TE=32 ms), followed by spontaneous neuronal activity (2.9%), thermal noise (2.1%), effects due to variability in physiological rates (respiration 0.9%, heartbeat 0.9%), and correlated with physiological cycles (0.6%). We suggest the selection and use of four lagged physiological noise regressors as an effective model to explain the variance related to fluctuations in the rates of respiration volume change and cardiac pulsation. Our results also indicate that, compared to the whole brain gray matter, the visual cortex has higher sensitivity to changes in both the rate of respiration and the spontaneous resting-state activity. Under the conditions of this study, spontaneous neuronal activity is one of the major contributors to the measured fMRI signal fluctuations, increasing almost twofold relative to earlier experiments under similar conditions at 3 T.  相似文献   

8.
Although it has been shown that the phase of the MR signal from the brain is particularly prone to variation due to respiration, the overall physiological information contained in phase time series is not well understood. Here, we explore the different physiological processes contributing to the phase time series noise, identify their spatiotemporal characteristics and examine their relationship to BOLD-related and non-BOLD-related physiological noise in the magnitude time series. This was performed by manipulating the contribution of physiological noise to the total signal variance by modulating the TE and voxel volume, and using a short TR in order to adequately sample physiological signal fluctuations. The phase and magnitude signals were compared both before and after removal of signal fluctuations at the primary respiratory and cardiac frequencies with RETROICOR. We found that the temporal phase noise increased with TE at a faster rate than predicted by 1/TSNR as a result of physiological noise. As suggested by previous studies, the primary contributor to phase physiological noise was respiration-related effects which were manifested at a large scale (>1 cm). Notably, RETROICOR removed respiration-related large-scale artifacts and this resulted in considerable improvements in the temporal phase stability (7–90%). Physiological noise in the magnitude time series after RETROICOR consisted of low-frequency BOLD-related fluctuations (<0.13 Hz) localized to gray matter and the vasculature, and fluctuations in the vasculature correlated with slow (<0.1 Hz) variations in respiration volume and cardiac rhythm. Physiological noise in the phase signal after RETROICOR also occurred in frequencies below 0.13 Hz and was consistent with (1) residual large-scale magneto-mechanical effects correlated with slow variations in respiration volume and cardiac rhythm over time, and (2) local scale (<1 cm) effects localized in gray matter and vasculature most likely due to vascular dephasing mediated by a BOLD susceptibility change. While BOLD-related magnitude noise exhibited a TE dependence similar to BOLD, the ‘BOLD-related’ noise in the phase data increased with increasing TE and thus caused the overall phase noise to increase at a faster rate with TE than predicted by 1/TSNR. Interestingly, the spatial specificity of this effect was more evident for the higher resolution phase data, as opposed to the magnitude data, suggesting that at a higher spatial resolution the phase signal may contain more information on physiological processes than the magnitude signal.  相似文献   

9.
Computer simulations have played a critical role in functional magnetic resonance imaging (fMRI) research, notably in the validation of new data analysis methods. Many approaches have been used to generate fMRI simulations, but there is currently no generic framework to assess how realistic each one of these approaches may be. In this article, a statistical technique called parametric bootstrap was used to generate a simulation database that mimicked the parameters found in a real database, which comprised 40 subjects and five tasks. The simulations were evaluated by comparing the distributions of a battery of statistical measures between the real and simulated databases. Two popular simulation models were evaluated for the first time by applying the bootstrap framework. The first model was an additive mixture of multiple components and the second one implemented a non-linear motion process. In both models, the simulated components included the following brain dynamics: a baseline, physiological noise, neural activation and random noise. These models were found to successfully reproduce the relative variance of the components and the temporal autocorrelation of the fMRI time series. By contrast, the level of spatial autocorrelation was found to be drastically low using the additive model. Interestingly, the motion process in the second model intrisically generated some slow time drifts and increased the level of spatial autocorrelations. These experiments demonstrated that the bootstrap framework is a powerful new tool that can pinpoint the respective strengths and limitations of simulation models.  相似文献   

10.
Recently, the possibility to use both magnitude and phase image sets for the statistical evaluation of fMRI has been proposed, with the prospective of increasing both statistical power and the spatial specificity. In the present work, several issues that affect the spatial and temporal stability in fMRI phase time series in the presence of physiologic noise processes are reviewed, discussed and illustrated by experiments performed at 3 T. The observed phase value is a fingerprint of the underlying voxel averaged magnetic field variations. Those related to physiological processes can be considered static or dynamic in relation to the temporal scale of a 2D acquisition and will play out on different spatial scales as well: globally across the entire images slice, and locally depending on the constituents and their relative fractions inside the MRI voxel. The 'static' respiration-induced effects lead to magneto-mechanic scan-to-scan variations in the global magnetic field but may also contribute to local BOLD fluctuations due to respiration-related variations in arterial carbon dioxide. Likewise, the 'dynamic' cardiac-related effects will lead to global susceptibility effects caused by pulsatile motion of the brain as well as local blood pressure-related changes in BOLD and changes in blood flow velocity. Finally, subject motion may lead to variations in both local and global tissue susceptibility that will be especially pronounced close to air cavities. Since dissimilar manifestations of physiological processes can be expected in phase and in magnitude images, a direct relationship between phase and magnitude scan-to-scan fluctuations cannot be assumed a priori. Therefore three different models were defined for the phase stability, each dependent on the relation between phase and magnitude variations and the best will depend on the underlying noise processes. By experiments on healthy volunteers at rest, we showed that phase stability depends on the type of post-processing and can be improved by reducing the low-frequency respiration-induced mechano-magnetic effects. Although the manifestations of physiological noise were in general more pronounced in phase than in magnitude images, due to phase wraps and global Bo effects, we suggest that a phase stability similar to that found in magnitude could theoretically be achieved by adequate correction methods. Moreover, as suggested by our experimental data regarding BOLD-related phase effects, phase stability could even supersede magnitude stability in voxels covering dense microvascular networks with BOLD-related fluctuations as the dominant noise contributor. In the interest of the quality of both BOLD-based and nc-MRI methods, future studies are required to find alternative methods that can improve phase stability, designed to match the temporal and spatial scale of the underlying neuronal activity.  相似文献   

11.
Principal component analysis (PCA) is one of several structure-seeking multivariate statistical techniques, exploratory as well as inferential, that have been proposed recently for the characterization and detection of activation in both PET and fMRI time series data. In particular, PCA is data driven and does not assume that the neural or hemodynamic response reaches some steady state, nor does it involve correlation with any pre-defined or exogenous experimental design template. In this paper, we present a generalized linear systems framework for PCA based on the singular value decomposition (SVD) model for representation of spatio-temporal fMRI data sets. Statistical inference procedures for PCA, including point and interval estimation will be introduced without the constraint of explicit hypotheses about specific task-dependent effects. The principal eigenvectors capture both the spatial and temporal aspects of fMRI data in a progressive fashion; they are inherently matched to unique and uncorrelated features and are ranked in order of the amount of variance explained. PCA also acts as a variation reduction technique, relegating most of the random noise to the trailing components while collecting systematic structure into the leading ones. Features summarizing variability may not directly be those that are the most useful. Further analysis is facilitated through linear subspace methods involving PC rotation and strategies of projection pursuit utilizing a reduced, lower-dimensional natural basis representation that retains most of the information. These properties will be illustrated in the setting of dynamic time-series response data from fMRI experiments involving pharmacological stimulation of the dopaminergic nigro-striatal system in primates.  相似文献   

12.
Functional magnetic resonance imaging (fMRI) is an effective tool for the measurement of brain neuronal activities. To date, several statistical methods have been proposed for analyzing fMRI datasets to select true active voxels among all the voxels appear to be positively activated. Finding a reliable and valid activation map is very important and becomes more crucial in clinical and neurosurgical investigations of single fMRI data, especially when pre-surgical planning requires accurate lateralization index as well as a precise localization of activation map.Defining a proper threshold to determine true activated regions, using common statistical processes, is a challenging task. This is due to a number of variation sources such as noise, artifacts, and physiological fluctuations in time series of fMRI data which affect spatial distribution of noise in an expected uniform activated region. Spatial smoothing methods are frequently used as a preprocessing step to reduce the effect of noise and artifacts. The smoothing may lead to a shift and enlargement of activation regions, and in some extend, unification of distinct regions.In this article, we propose a bootstrap resampling technique for analyzing single fMRI dataset with the aim of finding more accurate and reliable activated regions. This method can remove false positive voxels and present high localization accuracy in activation map without any spatial smoothing and statistical threshold setting.  相似文献   

13.
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.  相似文献   

14.
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.  相似文献   

15.
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.  相似文献   

16.
Analysis of resting-state functional magnetic resonance imaging (fMRI) data is based on detecting low-frequency signal fluctuations in functionally connected brain areas. These synchronous fluctuations in resting-state networks have been observed in several studies with healthy subjects. In this study, we explored if independent component analysis (ICA) can be used to localize the sensorimotor area from resting-state fMRI data in patients with brain tumors. Finger-tapping activation task and resting-state blood-oxygenation-level-dependent fMRI data were acquired from 8 patients with brain tumors and 10 healthy volunteers. Sensorimotor task independent components (ICtask) were used to verify resting-state independent components (ICrest) individually. In addition, sensorimotor ICrests were compared between the groups and no significant differences were detected in volume, spatial correlation or temporal correlation. These results show that it is possible to localize a sensorimotor area from resting-state data using ICA in patients with brain tumors. This offers a complementary method for assessing the sensorimotor area in subjects with brain tumors who have difficulties in performing motor paradigms.  相似文献   

17.
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.  相似文献   

18.
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.  相似文献   

19.
A method is described for denoising multiple-echo data sets using singular value decomposition (SVD). Images are acquired using a multiple gradient- or spin-echo sequence, and the variation of the signal with echo time (TE) in all pixels is subjected to SVD analysis to determine the components of the signal variation. The least significant components are associated with small singular values and tend to characterize the noise variation. Applying a "minimum variance" filter to the singular values suppresses the noise components in a way that optimally approximates the underlying noise-free images. The result is a reduction in noise in the individual TE images with minimal degradation of the spatial resolution and contrast. Phantom and in vivo results are presented.  相似文献   

20.
利用激光诱导击穿光谱技术结合机器学习算法,对东北5个产地(大兴安岭、集安、恒仁、石柱、抚松)的人参进行产地识别,建立了主成分分析算法分别结合反向传播(BP)神经网络和支持向量机算法的人参产地识别模型.实验采集了5个产地人参共657组在200-975 nm的激光诱导击穿光谱,经光谱数据预处理后,对C,Mg,Ca,Fe,H,N,O等元素的8条特征谱线进行主成分分析,原光谱数据的前3个主成分累积贡献率达到92.50%,且样品在主成分空间中呈现良好的聚集分类.降维后的前3个主成分以2∶1进行随机抽取,分别作为分类算法的训练集和测试集.实验结果表明主成分分析结合BP神经网络及支持向量机的平均识别率分别为99.08%和99.5%.发生误判的原因是集安和石柱两地地理环境的接近而导致的H,O两元素在Ca元素离子发射谱线下的归一化强度相似.本研究为激光诱导击穿光谱技术在人参产地的快速识别提供了方法和参考.  相似文献   

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