EvIdent: a functional magnetic resonance image analysis system

EvIdent (EVent IDENTification) is a user-friendly, algorithm-rich, exploratory data analysis software for quickly detecting, investigating, and visualizing novel events in a set of images as they evolve in time and/or frequency. For instance, in a series of functional magnetic resonance neuroimages, novelty may manifest itself as neural activations in a time course. The core of the system is an enhanced variant of the fuzzy c-means clustering algorithm. Fuzzy clustering obviates the need for models of the underlying requisite biological function, models that are often statistically suspect.     

模糊聚类分析在脑功能磁共振图像处理中的应用

模糊聚类分析作为模式识别中的一种重要的分类器,近年来在脑功能磁共振图像的处理与分析领域引起了极大的关注。在脑功能磁共振图像的处理与分析中应用模糊聚类技术需要解决的一个关键问题就是找出适合于脑功能磁共振图像处理的参数,如模糊指数、距离参数和聚类数等。如何寻找合适的参数,从而使得利用模糊聚类技术处理和分析脑功能磁共振图像得到最佳的聚类结果,成了目前模糊聚类技术研究的焦点问题。近年来模糊聚类分析在脑功能磁共振图像处理的应用中如何选择合适的参数问题进行了综述和讨论。     

An algorithm for automatic segmentation and classification of magnetic resonance brain images

In this article, we describe the development and validation of an automatic algorithm to segment brain from extracranial tissues, and to classify intracranial tissues as cerebrospinal fluid (CSF), gray matter (GM), white matter (WM) or pathology. T1 weighted spin echo, dual echo fast spin echo (T2 weighted and proton density (PD) weighted images) and fast Fluid Attenuated Inversion Recovery (FLAIR) magentic resonance (MR) images were acquired ino 100 normal patients and 9 multiple sclerosis (MS) patients. One of the normal studies had synthesized MS-like lesions superimposed. This allowed precise measurement of the accuracy of the classification. The 9 MS patients were imaged twice in one week. The algorithm was applied to these data sets to measure reproducibility. The accuracy was measured based on the synthetic lesion images, where the true voxel class was known. Ninety-six percent of normal intradural tissue voxels (GM, WM, and CSF) were labeled correctly, and 94% of pathological tissues were labeled correctly. A low coefficient of variation (COV) was found (mean, 4.1%) for measurement of brain tissues and pathology when comparing MRI scans on the 9 patients. A totally automatic segmentation algorithm has been described which accurately and reproducibly segments and classifies intradural tissues based on both synthetic and actual images.     

Robust image registration for functional magnetic resonance imaging of the brain

Motion-related artifacts are still a major problem in data analysis of functional magnetic resonance imaging (FMRI) studies of brain activation. However, the traditional image registration algorithm is prone to inaccuracy when there are residual variations owing to counting statistics, partial volume effects or biological variation. In particular, susceptibility artifacts usually result in remarkable signal intensity variance, and they can mislead the estimation of motion parameters. In this study, Two robust estimation algorithms for the registration of FMRI images are described. The first estimation algorithm was based on the Newton method and used Tukey's biweight objective function. The second estimation algorithm was based on the Levenberg-Marquardt technique and used a skipped mean objective function. The robust M-estimators can suppress the effects of the outliers by scaling down their error magnitudes or completely rejecting outliers using a weighting function. The proposed registration methods consisted of the following steps: fast segmentation of the brain region from noisy background as a preprocessing step; pre-registration of the volume centroids to provide a good initial estimation; and two robust estimation algorithms and a voxel sampling technique to find the affine transformation parameters. The accuracy of the algorithms was within 0.5 mm in translation and within 0.5° in rotation. For the FMRI data sets, the performance of the algorithms was visually compared with the AIR 2.0 software, which is a software for image registration, using colour-coded statistical mapping by the Kolmogorov-Smirov method. Experimental results showed, that the algorithms provided significant improvement in correcting motion-related artifacts and can enhance the detection of real brain activation.     

Fully automatic brain extraction algorithm for axial T2-weighted magnetic resonance images

In this paper we propose two brain extraction algorithms (BEA) for T2-weighted magnetic resonance imaging (MRI) scans. The T2-weighted image is first filtered with a low pass filter (LPF) to remove or subdue the background noise. Then the image is diffused to enhance the brain boundaries. Using Ridler’s method a threshold value for intensity is obtained. Using the threshold value a rough binary brain image is obtained. By performing morphological operations and using the largest connected component (LCC) analysis, a brain mask is obtained from which the brain is extracted. This method uses only 2D information of slices and is named as 2D-BEA. The concept of LCC failed in few slices. To overcome this problem, 3D information available in adjacent slices is used which resulted in 3D-BEA. Experimental results on 20 MRI data sets show that the proposed 3D-BEA gave excellent results. The performance of this 3D-BEA is better than 2D-BEA and other popular methods, brain extraction tool (BET) and brain surface extractor (BSE).     

基于层间先验知识从脑MRI图像中自动提取脑组织

目的从脑MRI图像中提取脑组织,解决边缘模糊时脑和非脑组织难以分离的问题。方法首先利用各向异性扩散滤波的方法对脑MRI图像进行去噪处理;然后利用形态学的方法对初始脑MRI图像进行脑组织提取,在此分割结果的基础上,利用相邻层脑形态差异较小的特点,实现结构元素的自适应选取,完成从脑MRI图像中逐层准确、自动提取脑组织。结果采用不同来源的数据对算法性能进行了测试,结果优于经典背散射电子成像(BSE)方法的分割结果。结论利用层间先验知识有利于实现边缘模糊的脑组织自动准确提取,且适用性较强。     

Multisensory functional magnetic resonance imaging: a future perspective

Advances in functional magnetic resonance imaging (fMRI) technology and analytic tools provide a powerful approach to unravel how the human brain combines the different sensory systems. In this perspective, we outline promising future directions of fMRI to make optimal use of its strengths in multisensory research, and to meet its weaker sides by combining it with other imaging modalities and computational modeling.     

Negative socio-emotional resonance in schizophrenia: a functional magnetic resonance imaging hypothesis

The aim of the present study is to use neuroscience theories about brain function (mirror-neurons MN) to draw inferences about the mechanisms supporting emotional resonance in two different groups of schizophrenia patients (with flat affect FA+ n = 13 and without flat affect FA- n = 11). We hypothesize that FA+ will not activate key brain areas involved in emotional processing. Conversely, FA- will have a functional mirror system for emotional resonance confirmed by activation of the prefrontal cortex and behavioral results. To test this hypothesis, we compared the two groups using blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) displaying a passive visual task (44 negative IAPS pictures and 44 neutral pictures). A random-effects analysis, for schizophrenia patients FA-, revealed significant loci of activation in the left mesial prefrontal (MPFC), right orbitofrontal (OFC) and left anterior cingulate cortices (ACC). Correlational analyses carried out between self-report ratings of negative feelings and BOLD signal changes revealed the existence of positive correlation in the LACC, LMPFC and ROFC. Conversely, FA+ did not show significant activation in the prefrontal cortex. We propose that negative emotional resonance induced by passively viewing negative pictures may be a form of "mirroring" that grounds negative feelings via an experiential mechanism. Hence, it could be argued that FA- were able to 'feel' emotions through this resonance behavior. Conversely, we suggest that the dysfunction seen in the FA+ group is a failure or distortion in the development of the MN system. This could be due to genetic or other endogenous causes, which affected prefrontal cortex MN involved in emotional resonance.     

功能磁共振成像熵连接工具箱的研制

目的:为了分析不同脑区间功能磁共振成像（fMRI）信号的效应连接状况,研制一个可计算时间序列间熵连接的工具箱。方法:在Windows环境下,MATLAB平台中编写熵连接代码,利用图形用户界面进行工具箱界面开发,通过设计控件的属性、编写回调函数及调用MATLAB内置程序计算熵连接。结果:该工具箱可实现时间序列间熵连接的计算,并可对结果进行统计分析。用户可输入已生成的脑区fMRI信号时间序列,也可以通过本工具箱生成感兴趣脑区的时间序列,进行计算熵连接。结论:该工具箱易于操作,界面友好,可极大地提高科研人员的效率。     

Cardiovascular risks and brain function: a functional magnetic resonance imaging study of executive function in older adults

Cardiovascular (CV) risk factors, such as hypertension, diabetes, and hyperlipidemia are associated with cognitive impairment and risk of dementia in older adults. However, the mechanisms linking them are not clear. This study aims to investigate the association between aggregate CV risk, assessed by the Framingham general cardiovascular risk profile, and functional brain activation in a group of community-dwelling older adults. Sixty participants (mean age: 64.6 years) from the Brain Health Study, a nested study of the Baltimore Experience Corps Trial, underwent functional magnetic resonance imaging using the Flanker task. We found that participants with higher CV risk had greater task-related activation in the left inferior parietal region, and this increased activation was associated with poorer task performance. Our results provide insights into the neural systems underlying the relationship between CV risk and executive function. Increased activation of the inferior parietal region may offer a pathway through which CV risk increases risk for cognitive impairment.     

Functional mapping of neural pathways in rodent brain in vivo using manganese-enhanced three-dimensional magnetic resonance imaging

This work presents three-dimensional MRI studies of rodent brain in vivo after focal and systemic administration of MnCl2. Particular emphasis is paid to the morphology and dynamics of Mn2+-induced MRI signal enhancements, and the physiological mechanisms underlying cerebral Mn2+ uptake and distribution. It turns out that intravitreal and intrahippocampal injections of MnCl2 emerge as useful tools for a delineation of major axonal connections in the intact central nervous system. Subcutaneous administrations may be exploited to highlight regions involved in fundamental brain functions such as the olfactory bulb, inferior colliculus, cerebellum and hippocampal formation. Specific insights into the processes supporting cerebral Mn2+ accumulation may be obtained by intraventricular MnCl2 injection as well as by pharmacologic modulation of, for example, hippocampal function. Taken together, Mn2+-enhanced MRI opens new ways for mapping functioning pathways in animal brain in vivo with applications ranging from assessments of transgenic animals to follow-up studies of animal models of human brain disorders.     

Functional magnetic resonance imaging of the human brain: data acquisition and analysis

It is now feasible to create spatial maps of activity in the human brain completely non-invasively using magnetic resonance imaging. Magnetic resonance imaging (MRI) images in which the spin magnetization is refocussed by gradient switching are sensitive to local changes in magnetic susceptibility, which can occur when the oxygenation state of blood changes. Cortical neural activity causes increases in blood flow, which usually result in changes in blood oxygenation. Hence changes of image intensity can be observed, given rise to the so-called Blood Oxygenation Level Dependent (BOLD) contrast technique. Use of echo-planar imaging methods (EPI) allows the monitoring over the entire brain of such changes in real time. A temporal resolution of 1–3 s, and a spatial resolution of 2 mm in-plane, can thus be obtained. Generally in a brain mapping experiment hundred of brain image volumes are acquired at repeat times of 1–6 s, while brain tasks are performed. The data are transformed into statistical maps of image difference, using the technique known as statistical parametric mapping (SPM). This method, based on robust multilinear regression techniques, has become the method of reference for analysis of positron emission tomography (PET) image data. The special characteristics of functional MRI data require some modification of SPM algorithms and strategies, and the MRI data must be gaussianized in time and space to conform to the assumptions of the statistics of Gaussian random fields. The steps of analysis comprise: removal of head movement effects, spatial smoothing, and statistical interference, which includes temporal smoothing and removal by fitting of temporal variations slower than the experimental paradigm. By these means, activation maps can be generated with great flexibility and statistical power, giving probability estimates for activated brain regions based on intensity or spatial extent, or both combined. Recent studies have shown that patterns of activation obtained in human brain for a given stimulus are independent of the order and spatial orientation with which MRI images are acquired, and hence that inflow effects are not important for EPI data with a TR much longer than T1.     

大脑功能磁共振成像基础研究进展

大脑功能区的定位一直是基础研究学者研究的热点，近年来功能磁共振成像(fMRI)作为一种新型无损伤技术，为大脑功能的基础研究提供了一个新的途径。fMRI以其高分辨成像技术适时反应脑神经活动时的功能变化，藉以了解在生命状态下大脑不同区域的主要功能和疾病时的功能改变。这是目前人们所掌握的唯一无侵入、无创伤、可精确定位人脑高级功能的研究手段：广义上fMRI方法包括脑血流测定技术、脑代谢测定技术、     

Working memory for order and the parietal cortex: an event-related functional magnetic resonance imaging study

Memory for order information has been tied to the frontal lobes, however, parietal activation is observed in many functional neuroimaging studies. Here we report functional magnetic resonance findings from an event-related experiment involving working memory for order. Five letters were presented for storage, followed after a delay by two probe items. Probe items could be separated by zero to three positions in the memory set and subjects had to indicate whether the items were in the correct order. Analyses indicate that activation in left parietal cortex shows a systematic decrease in activation with increasing probe distance. This finding is consistent with an earlier study in which we suggested that parietal cortical regions mediate the representation of order information via magnitude codes.     

MR-Eyetracker: a new method for eye movement recording in functional magnetic resonance imaging

 We present a method for recording saccadic and pursuit eye movements in the magnetic resonance tomograph designed for visual functional magnetic resonance imaging (fMRI) experiments. To reliably classify brain areas as pursuit or saccade related it is important to carefully measure the actual eye movements. For this purpose, infrared light, created outside the scanner by light-emitting diodes (LEDs), is guided via optic fibers into the head coil and onto the eye of the subject. Two additional fiber optical cables pick up the light reflected by the iris. The illuminating and detecting cables are mounted in a plastic eyepiece that is manually lowered to the level of the eye. By means of differential amplification, we obtain a signal that covaries with the horizontal position of the eye. Calibration of eye position within the scanner yields an estimate of eye position with a resolution of 0.2° at a sampling rate of 1000 Hz. Experiments are presented that employ echoplanar imaging with 12 image planes through visual, parietal and frontal cortex while subjects performed saccadic and pursuit eye movements. The distribution of BOLD (blood oxygen level dependent) responses is shown to depend on the type of eye movement performed. Our method yields high temporal and spatial resolution of the horizontal component of eye movements during fMRI scanning. Since the signal is purely optical, there is no interaction between the eye movement signals and the echoplanar images. This reasonably priced eye tracker can be used to control eye position and monitor eye movements during fMRI. Received: 7 September 1998 / Accepted: 19 February 1999     

Sleep stabilizes visuomotor adaptation memory: a functional magnetic resonance imaging study

The beneficial effect of sleep on motor memory consolidation is well known for motor sequence memory, but remains unsettled for visuomotor adaptation in humans. The aim of this study was to characterize more clearly the influence of sleep on consolidation of visuomotor adaptation using a between‐subjects functional magnetic resonance imaging (fMRI) design contrasting sleep to total sleep deprivation. Our behavioural results, based on seven different parameters, show that sleep stabilizes performance whereas sleep deprivation deteriorates it. During training, while a set of cerebellar, striatal and cortical areas is activated in proportion to performance improvement, the recruitment of the hippocampus and frontal cortex protects motor memory against the detrimental effects of sleep deprivation. During retest after sleep loss a cerebello–cortical network, usually involved in the earliest stage of learning, was recruited to perform the task. In contrast, no changes in cerebral activity were observed after sleep, suggesting that it may only support the stabilization of the visuomotor adaptation memory trace.     

Investigation of human brain hemodynamics by simultaneous near-infrared spectroscopy and functional magnetic resonance imaging

The aim of this study was to compare functional cerebral hemodynamic signals obtained simultaneously by near infrared spectroscopy (NIRS) and by functional magnetic resonance imaging (fMRI). The contribution of superficial layers (skin and skull) to the NIRS signal was also assessed. Both methods were used to generate functional maps of the motor cortex area during a periodic sequence of stimulation by finger motion and rest. In all subjects we found a good collocation of the brain activity centers revealed by both methods. We also found a high temporal correlation between the BOLD signal (fMRI) and the deoxy-hemoglobin concentration (NIRS) in the subjects who exhibited low fluctuations in superficial head tissues.     

Noxious hot and cold stimulation produce common patterns of brain activation in humans: a functional magnetic resonance imaging study

We used functional magnetic resonance imaging (fMRI) to determine whether similar brain regions activate during noxious hot and cold stimulation. Six male subjects underwent whole brain fMRI during phasic delivery of noxious hot (46 degrees C) and noxious cold (5 degrees C) stimulation to the dorsum of the left hand. Mid-brain regions activated included thalamus, basal ganglia and insula. Cortical areas activated included cingulate, somatosensory, premotor and motor cortices, as well as prefrontal and inferior parietal cortex. Most regions activated bilaterally but with stronger activation contralateral to the stimulus. Noxious cold stimulation produced significantly increased volumes of activation compared to noxious heat in prefrontal areas only. Our results suggest a similar network of regions activate common to the perception of pain produced by either noxious hot or cold stimulation.     

Olfactory-induced brain activity in Parkinson's disease relates to the expression of event-related potentials: a functional magnetic resonance imaging study

Olfactory disorders are common in patients with idiopathic Parkinson's disease (IPD). In IPD patients with hyposmia olfactory event-related potentials (ERPs) are typically found to be delayed or absent. Altered ERPs in IPD patients may also be consistent with reduced neuronal activity in the medial temporal lobe following olfactory stimulation, as demonstrated by functional magnetic resonance imaging (fMRI). We analyzed ERPs and fMRI scans of hyposmic IPD patients (n=18) to gain further insight about the brain regions involved in generation of olfactory ERPs. Patients were separated into two groups (n=9 per group), based on the detectability (+) or non-detectability (−) of ERPs. Central activation during olfactory stimulation was examined using fMRI. Both ERP+ and ERP− patients showed activity in brain areas relevant to olfactory processing, such as the amygdala, parahippocampal regions, and temporal regions (BA 37, 21/22). Comparison of both groups revealed higher activation in ERP+ patients, especially in the amygdala, parahippocampal cortex, inferior frontal gyrus (BA 47), insula, cingulate gyrus, striatum, and inferior temporal gyrus. The relationship between the expression of olfactory ERPs and cortical activation patterns seen during olfactory stimulation in fMRI in IPD patients supports the idea that ERPs are a sensitive marker of neurodegeneration in olfactory regions. In accordance with current neuropathological staging concepts, olfactory ERPs may be reflecting pathological changes in olfactory regions, independent of the typically observed nigro-striatal degeneration in IPD. Reduced activation of primary olfactory areas in the ERP-group may reflect a severe disruption of olfactory processing in these patients.