Eyes-Open/Eyes-Closed Dataset Sharing for Reproducibility Evaluation of Resting State fMRI Data Analysis Methods

Springer Science and Business Media LLC - Tập 11 Số 4 - Trang 469-476 - 2013
Dongqiang Liu1, Zhang-Ye Dong2, Xi‐Nian Zuo3, Jue Wang1,2, Yu‐Feng Zang1,2
1Center for Cognition and Brain Disorders, Hangzhou Normal University, Hangzhou, China
2National Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
3Laboratory for Functional Connectome and Development, Key Laboratory of Behavioral Science, Institute of Psychology, Chinese Academy of Sciences, Beijing, China

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Tài liệu tham khảo

Albert, N. B., Robertson, E. M., & Miall, R. C. (2009). The resting human brain and motor learning. Current Biology, 19(12), 1023–1027.

Barnes, A., Bullmore, E. T., & Suckling, J. (2009). Endogenous human brain dynamics recover slowly following cognitive effort. PLoS One, 4(8), e6626.

Beckmann, C. F., DeLuca, M., Devlin, J. T., & Smith, S. M. (2005). Investigations into resting-state connectivity using independent component analysis. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360(1457), 1001–1013.

Biswal, B., Yetkin, F. Z., Haughton, V. M., & Hyde, J. S. (1995). Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magnetic Resonance in Medicine, 34(4), 537–541.

Castellanos, F. X., Margulies, D. S., Kelly, C., Uddin, L. Q., Ghaffari, M., et al. (2008). Cingulate-precuneus interactions: a new locus of dysfunction in adult attention-deficit/hyperactivity disorder. Biological Psychiatry, 63(3), 332–337.

Cole, D. M., Smith, S. M., & Beckmann, C. F. (2010). Advances and pitfalls in the analysis and interpretation of resting-state fMRI data. Frontiers in Systems Neuroscience, 4, 8.

Cordes, D., Haughton, V. M., Arfanakis, K., Wendt, G. J., Turski, P. A., Moritz, C. H., Quigley, M. A., & Meyerand, M. E. (2000). Mapping functionally related regions of brain with functional connectivity MR imaging. American Journal of Neuroradiology, 21(9), 1636–1644.

Cox, R. W. (1996). AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. Computers and Biomedical Research, 29(3), 162–173.

Di Martino, A., Scheres, A., Margulies, D. S., Kelly, A. M., Uddin, L. Q., Shehzad, Z., Biswal, B., Walters, J. R., Castellanos, F. X., & Milham, M. P. (2008). Functional connectivity of human striatum: a resting state FMRI study. Cerebral Cortex, 18(12), 2735–2747.

Fox, M. D., Snyder, A. Z., Vincent, J. L., Corbetta, M., Van Essen, D. C., & Raichle M. E. (2005). The human brain is intrinsically organized into dynamic, anticorrelated functional networks. Proceedings of the National Academy of Sciences in United States of America, 105(27), 9673–9678.

Fox, M. D., Corbetta, M., Snyder, A. Z., Vincent, J. L., & Raichle, M. E. (2006). Spontaneous neuronal activity distinguishes human dorsal and ventral attention systems. Proceedings of the National Academy of Sciences in United States of America, 103(26), 10046–10051.

Friston, K. J., Holmes, A. P., Price, C. J., Buchel, C., & Worsley, K. J. (1999). Multisubject fMRI studies and conjunction analyses. NeuroImage, 10(4), 385–396.

Greicius, M. D., Krasnow, B., Reiss, A. L., & Menon, V. (2003). Functional connectivity in the resting brain: a network analysis of the default mode hypothesis. Proceedings of the National Academy of Sciences in United States of America, 100(1), 253–258.

Grigg, O., & Grady, C. L. (2010). Task-related effects on the temporal and spatial dynamics of resting-state functional connectivity in the default network. PLoS One, 5(10), e13311.

Hoptman, M. J., Zuo, X. N., Butler, P. D., Javitt, D. C., D’Angelo, D., Mauro, C. J., & Milham, M. P. (2010). Amplitude of low-frequency oscillations in schizophrenia: a resting state fMRI study. Schizophrenia Research, 117(1), 13–20.

Kendall, M., & Gibbons, J. D. (1990). Rank correlation methods. Oxford: Oxford University Press.

Lai, M. C., Lombardo, M. V., Chakrabarti, B., Sadek, S. A., Pasco, G., Wheelwright, S. J., Bullmore, E. T., Baron-Cohen, S., & Suckling, J. (2010). A shift to randomness of brain oscillations in people with autism. Biological Psychiatry, 68(12), 1092–1099.

Ledberg, A., Akerman, S., & Roland, P. E. (1998). Estimation of the probabilities of 3D clusters in functional brain images. NeuroImage, 8(2), 113–128.

Lowe, M. J., Mock, B. J., & Sorenson, J. A. (1998). Functional connectivity in single and multislice echoplanar imaging using resting-state fluctuations. NeuroImage, 7(2), 119–132.

Machielsen, W. C., Rombouts, S. A., Barkhof, F., Scheltens, P., & Witter, M. P. (2000). FMRI of visual encoding: reproducibility of activation. Human Brain Mapping, 9(3), 156–164.

Margulies, D. S., Bottger, J., Long, X., Lv, Y., Kelly, C., Schafer, A., Goldhahn, D., Abbushi, A., Milham, M. P., Lohmann, G., & Villringer, A. (2010). Resting developments: a review of fMRI post-processing methodologies for spontaneous brain activity. Magma, 23(5–6), 289–307.

Nichols, T., Brett, M., Andersson, J., Wager, T., & Poline, J. B. (2005). Valid conjunction inference with the minimum statistic. NeuroImage, 25(3), 653–660.

Paakki, J. J., Rahko, J., Long, X., Moilanen, I., Tervonen, O., Nikkinen, J., Starck, T., Remes, J., Hurtig, T., Haapsamo, H., Jussila, K., Kuusikko-Gauffin, S., Mattila, M. L., Zang, Y., & Kiviniemi, V. (2010). Alterations in regional homogeneity of resting-state brain activity in autism spectrum disorders. Brain Research, 1321, 169–179.

Press, W. H. T. S., Vetterling, W. T., & Flannery, B. P. (1992). Numerical Recipes in C (2nd ed.). Cambridge: Cambridge University Press.

Raichle, M. E., MacLeod, A. M., Snyder, A. Z., Powers, W. J., Gusnard, D. A., & Shulman, G. L. (2001). A default mode of brain function. Proceedings of the National Academy of Sciences in United States of America, 98(2), 676–682.

Salvador, R., Martinez, A., Pomarol-Clotet, E., Sarro, S., Suckling, J., & Bullmore, E. (2007). Frequency based mutual information measures between clusters of brain regions in functional magnetic resonance imaging. NeuroImage, 35(1), 83–88.

Shehzad, Z., Kelly, A. M., Reiss, P. T., Gee, D. G., Gotimer, K., Uddin, L. Q., Lee, S. H., Margulies, D. S., Roy, A. K., Biswal, B. B., Petkova, E., Castellanos, F. X., & Milham, M. P. (2009). The resting brain: unconstrained yet reliable. Cerebral Cortex, 19(10), 2209–2229.

Sheline, Y. I., Raichle, M. E., Snyder, A. Z., Morris, J. C., Head, D., et al. (2010). Amyloid plaques disrupt resting state default mode network connectivity in cognitively normal elderly. Biological Psychiatry, 67(6), 584–587.

Song, X. W., Dong, Z. Y., Long, X. Y., Li, S. F., Zuo, X. N., Zhu, C. Z., He, Y., Yan, C. G., & Zang, Y. F. (2011). REST: a toolkit for resting-state functional magnetic resonance imaging data processing. PLoS One, 6(9), e25031.

Stiers, P., Mennes, M., & Sunaert, S. (2010). Distributed task coding throughout the multiple demand network of the human frontal-insular cortex. NeuroImage, 52(1), 252–262.

Strother, S. C., Anderson, J., Hansen, L. K., Kjems, U., Kustra, R., et al. (2002). The quantitative evaluation of functional neuroimaging experiments: the NPAIRS data analysis framework. NeuroImage, 15(4), 747–771.

Tambini, A., Ketz, N., & Davachi, L. (2010). Enhanced brain correlations during rest are related to memory for recent experiences. Neuron, 65(2), 280–290.

Van Dijk, K. R., Hedden, T., Venkataraman, A., Evans, K. C., Lazar, S. W., & Buckner, R. L. (2010). Intrinsic functional connectivity as a tool for human connectomics: theory, properties, and optimization. Journal of Neurophysiology, 103(1), 297–321.

Waites, A. B., Stanislavsky, A., Abbott, D. F., & Jackson, G. D. (2005). Effect of prior cognitive state on resting state networks measured with functional connectivity. Human Brain Mapping, 24(1), 59–68.

Wang, K., Yu, C., Xu, L., Qin, W., Li, K., Xu, L., & Jiang, T. (2009). Offline memory reprocessing: involvement of the brain’s default network in spontaneous thought processes. PLoS One, 4(3), e4867.

Wang, L., Yu, C., Chen, H., Qin, W., He, Y., Fan, F., Zhang, Y., Wang, M., Li, K., Zang, Y., Woodward, T. S., & Zhu, C. (2010). Dynamic functional reorganization of the motor execution network after stroke. Brain, 133(Pt 4), 1224–1238.

Wu, T., Long, X., Zang, Y., Wang, L., Hallett, M., Li, K., & Chan, P. (2009). Regional homogeneity changes in patients with Parkinson’s disease. Human Brain Mapping, 30(5), 1502–1510.

Yan, C., & Zang, Y. (2010). DPARSF: A MATLAB toolbox for “Pipeline” data analysis of resting-state fMRI. Frontiers in Systems Neuroscience, 4, 13.

Yan, C., Liu, D., He, Y., Zou, Q., Zhu, C., et al. (2009). Spontaneous brain activity in the default mode network is sensitive to different resting-state conditions with limited cognitive load. PLoS One, 4(5), e5743.

Yang, H., Long, X. Y., Yang, Y., Yan, H., Zhu, C. Z., Zhou, X. P., Zang, Y. F., & Gong, Q. Y. (2007). Amplitude of low frequency fluctuation within visual areas revealed by resting-state functional MRI. NeuroImage, 36(1), 144–152.

Zang, Y., Jiang, T., Lu, Y., He, Y., & Tian, L. (2004). Regional homogeneity approach to fMRI data analysis. NeuroImage, 22(1), 394–400.

Zang, Y. F., He, Y., Zhu, C. Z., Cao, Q. J., Sui, M. Q., Liang, M., Tian, L. X., Jiang, T. Z., & Wang, Y. F. (2007). Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI. Brain & Development, 29(2), 83–91.

Zhang, D., & Raichle, M. E. (2010). Disease and the brain’s dark energy. Nature Reviews. Neurology, 6(1), 15–28.

Zuo, X. N., Di Martino, A., Kelly, C., Shehzad, Z. E., Gee, D. G., Klein, D. F., Castellanos, F. X., Biswal, B. B., & Milham, M. P. (2010a). The oscillating brain: complex and reliable. NeuroImage, 49(2), 1432–1445.

Zuo, X. N., Kelly, C., Adelstein, J. S., Klein, D. F., Castellanos, F. X., & Milham, M. P. (2010b). Reliable intrinsic connectivity networks: test-retest evaluation using ICA and dual regression approach. NeuroImage, 49(3), 2163–2177.