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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 36

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          Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI.

          In children with attention deficit hyperactivity disorder (ADHD), functional neuroimaging studies have revealed abnormalities in various brain regions, including prefrontal-striatal circuit, cerebellum, and brainstem. In the current study, we used a new marker of functional magnetic resonance imaging (fMRI), amplitude of low-frequency (0.01-0.08Hz) fluctuation (ALFF) to investigate the baseline brain function of this disorder. Thirteen boys with ADHD (13.0+/-1.4 years) were examined by resting-state fMRI and compared with age-matched controls. As a result, we found that patients with ADHD had decreased ALFF in the right inferior frontal cortex, [corrected] and bilateral cerebellum and the vermis as well as increased ALFF in the right anterior cingulated cortex, left sensorimotor cortex, and bilateral brainstem. This resting-state fMRI study suggests that the changed spontaneous neuronal activity of these regions may be implicated in the underlying pathophysiology in children with ADHD.
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            Spontaneous low-frequency BOLD signal fluctuations: an fMRI investigation of the resting-state default mode of brain function hypothesis.

            Recent neuroimaging studies have lead to the proposal that rest is characterized by an organized, baseline level of activity, a default mode of brain function that is suspended during specific goal-oriented mental activity. Previous studies have shown that the primary function subserved by the default mode is that of an introspectively oriented, self-referential mode of mental activity. The default mode of brain function hypothesis is readdressed from the perspective of the presence of low-frequency blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) signal changes (0.012-0.1 Hz) in the resting brain. The results show that the brain during rest is not tonically active in a single mode of brain function. Rather, the findings presented here suggest that the brain recurrently toggles between an introspectively oriented mode (default mode) and a state-of-mind that tentatively might be interpreted as an extrospectively oriented mode that involves a readiness and alertness to changes in the external and internal environment.
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              Functional connectivity in single and multislice echoplanar imaging using resting-state fluctuations.

              A previous report of correlations in low-frequency resting-state fluctuations between right and left hemisphere motor cortices in rapidly sampled single-slice echoplanar data is confirmed using a whole-body echoplanar MRI scanner at 1.5 T. These correlations are extended to lower sampling rate multislice echoplanar acquisitions and other right/left hemisphere-symmetric functional cortices. The specificity of the correlations in the lower sampling-rate acquisitions is lower due to cardiac and respiratory-cycle effects which are aliased into the pass-band of the low-pass filter. Data are combined for three normal right-handed male subjects. Correlations to left hemisphere motor cortex, visual cortex, and amygdala are measured in long resting-state scans.
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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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