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      • Record: found
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      REST: A Toolkit for Resting-State Functional Magnetic Resonance Imaging Data Processing

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          Abstract

          Resting-state fMRI (RS-fMRI) has been drawing more and more attention in recent years. However, a publicly available, systematically integrated and easy-to-use tool for RS-fMRI data processing is still lacking. We developed a toolkit for the analysis of RS-fMRI data, namely the RESting-state fMRI data analysis Toolkit (REST). REST was developed in MATLAB with graphical user interface (GUI). After data preprocessing with SPM or AFNI, a few analytic methods can be performed in REST, including functional connectivity analysis based on linear correlation, regional homogeneity, amplitude of low frequency fluctuation (ALFF), and fractional ALFF. A few additional functions were implemented in REST, including a DICOM sorter, linear trend removal, bandpass filtering, time course extraction, regression of covariates, image calculator, statistical analysis, and slice viewer (for result visualization, multiple comparison correction, etc.). REST is an open-source package and is freely available at http://www.restfmri.net.

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          Most cited references 54

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          Advances in functional and structural MR image analysis and implementation as FSL.

          The techniques available for the interrogation and analysis of neuroimaging data have a large influence in determining the flexibility, sensitivity, and scope of neuroimaging experiments. The development of such methodologies has allowed investigators to address scientific questions that could not previously be answered and, as such, has become an important research area in its own right. In this paper, we present a review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB). This research has focussed on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data. The majority of the research laid out in this paper has been implemented as freely available software tools within FMRIB's Software Library (FSL).
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            A default mode of brain function.

            A baseline or control state is fundamental to the understanding of most complex systems. Defining a baseline state in the human brain, arguably our most complex system, poses a particular challenge. Many suspect that left unconstrained, its activity will vary unpredictably. Despite this prediction we identify a baseline state of the normal adult human brain in terms of the brain oxygen extraction fraction or OEF. The OEF is defined as the ratio of oxygen used by the brain to oxygen delivered by flowing blood and is remarkably uniform in the awake but resting state (e.g., lying quietly with eyes closed). Local deviations in the OEF represent the physiological basis of signals of changes in neuronal activity obtained with functional MRI during a wide variety of human behaviors. We used quantitative metabolic and circulatory measurements from positron-emission tomography to obtain the OEF regionally throughout the brain. Areas of activation were conspicuous by their absence. All significant deviations from the mean hemisphere OEF were increases, signifying deactivations, and resided almost exclusively in the visual system. Defining the baseline state of an area in this manner attaches meaning to a group of areas that consistently exhibit decreases from this baseline, during a wide variety of goal-directed behaviors monitored with positron-emission tomography and functional MRI. These decreases suggest the existence of an organized, baseline default mode of brain function that is suspended during specific goal-directed behaviors.
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              The human brain is intrinsically organized into dynamic, anticorrelated functional networks.

              During performance of attention-demanding cognitive tasks, certain regions of the brain routinely increase activity, whereas others routinely decrease activity. In this study, we investigate the extent to which this task-related dichotomy is represented intrinsically in the resting human brain through examination of spontaneous fluctuations in the functional MRI blood oxygen level-dependent signal. We identify two diametrically opposed, widely distributed brain networks on the basis of both spontaneous correlations within each network and anticorrelations between networks. One network consists of regions routinely exhibiting task-related activations and the other of regions routinely exhibiting task-related deactivations. This intrinsic organization, featuring the presence of anticorrelated networks in the absence of overt task performance, provides a critical context in which to understand brain function. We suggest that both task-driven neuronal responses and behavior are reflections of this dynamic, ongoing, functional organization of the brain.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2011
                20 September 2011
                : 6
                : 9
                Affiliations
                [1 ]State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
                [2 ]Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
                [3 ]Institute of Psychology, Chinese Academy of Sciences, Beijing, China
                [4 ]Center for Cognition and Brain Disorders and The Affiliated Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, China
                The University of Melbourne, Australia
                Author notes

                Conceived and designed the experiments: Y-FZ X-WS C-GY C-ZZ YH Z-YD X-NZ. Performed the experiments: X-WS Z-YD C-GY X-YL S-FL YH X-NZ. Analyzed the data: X-WS X-YL S-FL Z-YD C-GY. Contributed reagents/materials/analysis tools: X-WS X-YL S-FL Z-YD C-GY. Wrote the paper: X-WS Z-YD C-GY X-YL S-FL X-NZ YH C-ZZ Y-FZ.

                Article
                PONE-D-11-09456
                10.1371/journal.pone.0025031
                3176805
                21949842
                Song et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                Page count
                Pages: 12
                Categories
                Research Article
                Biology
                Neuroscience
                Neuroimaging
                Fmri
                Computer Science
                Computer Applications
                Web-Based Applications
                Medicine
                Neurology
                Neuroimaging

                Uncategorized

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