Resting developments: a review of fMRI post-processing methodologies for spontaneous brain activity
Tóm tắt
Từ khóa
Tài liệu tham khảo
Friston KJ, Frith CD, Liddle PF, Frackowiak RS (1993) Functional connectivity: the principal-component analysis of large (PET) data sets. J Cereb Blood Flow Metab 13: 5–14
Buckner RL, Vincent JL (2007) Unrest at rest: default activity and spontaneous network correlations. Neuroimage 37: 1091–1096 discussion 1097–1099
Morcom AM, Fletcher PC (2007) Does the brain have a baseline? why we should be resisting a rest. Neuroimage 37: 1073–1082
Fox MD, Raichle ME (2007) Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nat Rev Neurosci 8: 700–711
Lohmann G, Hoehl S, Brauer J, Danielmeier C, Bornkessel-Schlesewsky I, Bahlmann J, Turner R, Friederici A (2010) Setting the frame: the human brain activates a basic low-frequency network for language processing. Cereb Cortex 20: 1286–1292
Dijk KRAV, Hedden T, Venkataraman A, Evans KC, Lazar SW, Buckner RL (2010) Intrinsic functional connectivity as a tool for human connectomics: theory, properties, and optimization. J Neurophysiol 103: 297–321
Weissenbacher A, Kasess C, Gerstl F, Lanzenberger R, Moser E, Windischberger C (2009) Correlations and anticorrelations in resting-state functional connectivity MRI: a quantitative comparison of preprocessing strategies. Neuroimage 47: 1408–1416
Gavrilescu M, Stuart GW, Rossell S, Henshall K, McKay C, Sergejew AA, Copolov D, Egan GF (2008) Functional connectivity estimation in fMRI data: influence of preprocessing and time course selection. Hum Brain Mapp 29: 1040–1052
Chang C, Glover GH (2009) Effects of model-based physiological noise correction on default mode network anti-correlations and correlations. Neuroimage 47: 1448–1459
Fox MD, Zhang D, Snyder AZ, Raichle ME (2009) The global signal and observed anticorrelated resting state brain networks. J Neurophysiol 101: 3270–3283
Auer DP (2008) Spontaneous low-frequency blood oxygenation level-dependent fluctuations and functional connectivity analysis of the ‘resting’ brain. Magn Reson Imaging 26: 1055–1064
Li K, Guo L, Nie J, Li G, Liu T (2009) Review of methods for functional brain connectivity detection using fMRI. Comput Med Imaging Graph 33: 131–139
Cole DM, Smith SM, Beckmann CF (2010) Advances and pitfalls in the analysis and interpretation of resting-state fmri data. Front Syst Neurosci 4: 8
Liu Y, Wang K, Yu C, He Y, Zhou Y, Liang M, Wang L, Jiang T (2008) Regional homogeneity, functional connectivity and imaging markers of Alzheimer’s disease: a review of resting-state fmri studies. Neuropsychologia 46: 1648–1656
Fornito A, Bullmore ET (2010) What can spontaneous fluctuations of the blood oxygenation-level-dependent signal tell us about psychiatric disorders?. Curr Opin Psychiatry 23(3): 239–249
Biswal B, Zerrin Yetkin F, Haughton VM, Hyde JS (1995) Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magn Reson Med Sci 34: 537–541
Zhou D, Thompson WK, Siegle G (2009) MATLAB toolbox for functional connectivity. Neuroimage 47: 1590–1607
Shulman GL, Fiez JA, Corbetta M, Buckner RL, Miezin FM, Raiche ME, Petersen SE (1997) Common blood flow changes across visual tasks: II. decreases in cerebral cortex. J Cognive Neurosci 9: 648–663
Gusnard DA, Raichle ME (2001) Searching for a baseline: functional imaging and the resting human brain. Nat Rev Neurosci 2: 685–694
Buckner RL, Andrews-Hanna JR, Schacter DL (2008) The brain’s default network: anatomy, function, and relevance to disease. Ann N Y Acad Sci 1124: 1–38
Zhong Y, Wang H, Lu G, Zhang Z, Jiao Q, Liu Y (2009) Detecting functional connectivity in fMRI using PCA and regression analysis. Brain Topogr 22: 134–144
Müller K, Mildner T, Lohmann G, von Cramon DY (2003) Investigating the stimulus-dependent temporal dynamics of the bold signal using spectral methods. J Magn Reson Imaging 17: 375–382
Sun FT, Miller LM, D’Esposito M (2004) Measuring interregional functional connectivity using coherence and partial coherence analyses of fMRI data. Neuroimage 21: 647–658
Cordes D, Haughton VM, Arfanakis K, Carew JD, Turski PA, Moritz CH, Quigley MA, Meyerand ME (2001) Frequencies contributing to functional connectivity in the cerebral cortex in “resting-state” data. AJNR Am J Neuroradiol 22: 1326–1333
Zuo XN, Martino AD, Kelly C, Shehzad ZE, Gee DG, Klein DF, Castellanos FX, Biswal BB, Milham MP (2010) The oscillating brain: complex and reliable. Neuroimage 49: 1432–1445
Wu CW, Gu H, Lu H, Stein EA, Chen JHH, Yang Y (2008) Frequency specificity of functional connectivity in brain networks. Neuroimage 42: 1047–1055
Salvador R, Martinez A, Pomarol-Clotet E, Gomar J, Vila F, Sarro S, Capdevila A, Bullmore E (2008) A simple view of the brain through a frequency-specific functional connectivity measure. Neuroimage 39: 279–289
Duff EP, Johnston LA, Xiong J, Fox PT, Mareels I, Egan GF (2008) The power of spectral density analysis for mapping endogenous bold signal fluctuations. Hum Brain Mapp 29: 778–790
Barnes A, Bullmore ET, Suckling J (2009) Endogenous human brain dynamics recover slowly following cognitive effort. PLoS One 4: e6626
Sun FT, Miller LM, D’Esposito M (2005) Measuring temporal dynamics of functional networks using phase spectrum of fMRI data. Neuroimage 28: 227–237
Fisher RA (1924) The distribution of the partial correlation coefficient. Metron 3: 329–332
Zhang ZQQ, Lu GMM, Zhong Y, Tan QFF, Zhu JGG, Jiang L, Chen ZLL, Wang ZQQ, Shi JXX, Zang YFF, Liu YJJ (2008) Application of amplitude of low-frequency fluctuation to the temporal lobe epilepsy with bilateral hippocampal sclerosis: an fMRI study. Zhonghua Yi Xue Za Zhi 88: 1594–1598
Fransson P, Marrelec G (2008) The precuneus/posterior cingulate cortex plays a pivotal role in the default mode network: Evidence from a partial correlation network analysis. Neuroimage 42: 1178–1184
Granger CWJ (1969) Investigating causal relations by econometric models and cross-spectral methods. Econometrica 37: 424–438
Sridharan D, Levitin DJ, Menon V (2008) A critical role for the right fronto-insular cortex in switching between central-executive and default-mode networks. Proc Natl Acad Sci USA 105: 12569–12574
Uddin LQ, Kelly AMC, Biswal BB, Castellanos FX, Milham MP (2009) Functional connectivity of default mode network components: correlation, anticorrelation, and causality. Hum Brain Mapp 30: 625–637
Stevens MC, Pearlson GD, Calhoun VD (2009) Changes in the interaction of resting-state neural networks from adolescence to adulthood. Hum Brain Mapp 30: 2356–2366
Hemmelmann D, Ungureanu M, Hesse W, Wstenberg T, Reichenbach JR, Witte OW, Witte H, Leistritz L (2009) Modelling and analysis of time-variant directed interrelations between brain regions based on bold-signals. Neuroimage 45: 722–737
Xiong J, Parsons LM, Gao JH, Fox PT (1999) Interregional connectivity to primary motor cortex revealed using MRI resting state images. Hum Brain Mapp 8: 151–156
Lowe MJ, Mock BJ, Sorenson JA (1998) Functional connectivity in single and multislice echoplanar imaging using resting-state fluctuations. Neuroimage 7: 119–132
Cordes D, Haughton VM, Arfanakis K, Wendt GJ, Turski PA, Moritz CH, Quigley MA, Meyerand ME (2000) Mapping functionally related regions of brain with functional connectivity MR imaging. AJNR Am J Neuroradiol 21: 1636–1644
Hampson M, Olson IR, Leung HCC, Skudlarski P, Gore JC (2004) Changes in functional connectivity of human MT/V5 with visual motion input. Neuroreport 15: 1315–1319
Lowe MJ, Dzemidzic M, Lurito JT, Mathews VP, Phillips MD (2000) Correlations in low-frequency bold fluctuations reflect cortico-cortical connections. Neuroimage 12: 582–587
Hampson M, Peterson BS, Skudlarski P, Gatenby JC, Gore JC (2002) Detection of functional connectivity using temporal correlations in MR images. Hum Brain Mapp 15: 247–262
Allen G, McColl R, Barnard H, Ringe WK, Fleckenstein J, Cullum CM (2005) Magnetic resonance imaging of cerebellar-prefrontal and cerebellar-parietal functional connectivity. Neuroimage 28: 39–48
Greicius MD, Krasnow B, Reiss AL, Menon V (2003) Functional connectivity in the resting brain: a network analysis of the default mode hypothesis. Proc Natl Acad Sci USA 100: 253–258
Gusnard DA, Akbudak E, Shulman GL, Raichle ME (2001) Medial prefrontal cortex and self-referential mental activity: relation to a default mode of brain function. Proc Natl Acad Sci USA 98: 4259–4264
Raichle ME, MacLeod AM, Snyder AZ, Powers WJ, Gusnard DA, Shulman GL (2001) A default mode of brain function. Proc Natl Acad Sci USA 98: 676–682
Postuma RB, Dagher A (2006) Basal ganglia functional connectivity based on a meta-analysis of 126 positron emission tomography and functional magnetic resonance imaging publications. Cereb Cortex 16: 1508–1521
Bush G, Luu P, Posner MI (2000) Cognitive and emotional influences in anterior cingulate cortex. Trends Cogn Sci 4: 215–222
Stoodley CJ, Schmahmann JD (2009) Functional topography in the human cerebellum: a meta-analysis of neuroimaging studies. Neuroimage 44: 489–501
Martino AD, Scheres A, Margulies DS, Kelly AMC, Uddin LQ, Shehzad Z, Biswal B, Walters JR, Castellanos FX, Milham MP (2008) Functional connectivity of human striatum: a resting state fMRI study. Cereb Cortex 18: 2735–2747
Robinson S, Basso G, Soldati N, Sailer U, Jovicich J, Bruzzone L, Kryspin-Exner I, Bauer H, Moser E (2009) A resting state network in the motor control circuit of the basal ganglia. BMC Neurosci 10: 137
Margulies DS, Kelly AMC, Uddin LQ, Biswal BB, Castellanos FX, Milham MP (2007) Mapping the functional connectivity of anterior cingulate cortex. Neuroimage 37: 579–588
Krienen FM, Buckner RL (2009) Segregated fronto-cerebellar circuits revealed by intrinsic functional connectivity. Cereb Cortex 19: 2485–2497
O’Reilly JX, Beckmann CF, Tomassini V, Ramnani N, Johansen-Berg H (2010) Distinct and overlapping functional zones in the cerebellum defined by resting state functional connectivity. Cereb Cortex 20: 953–965
Roy AK, Shehzad Z, Margulies DS, Kelly AMC, Uddin LQ, Gotimer K, Biswal BB, Castellanos FX, Milham MP (2009) Functional connectivity of the human amygdala using resting state fMRI. Neuroimage 45: 614–626
Etkin A, Prater KE, Schatzberg AF, Menon V, Greicius MD (2009) Disrupted amygdalar subregion functional connectivity and evidence of a compensatory network in generalized anxiety disorder. Arch Gen Psychiatry 66: 1361–1372
Kahn I, Andrews-Hanna JR, Vincent JL, Snyder AZ, Buckner RL (2008) Distinct cortical anatomy linked to subregions of the medial temporal lobe revealed by intrinsic functional connectivity. J Neurophysiol 100: 129–139
Eckert MA, Kamdar NV, Chang CE, Beckmann CF, Greicius MD, Menon V (2008) A cross-modal system linking primary auditory and visual cortices: evidence from intrinsic fMRI connectivity analysis. Hum Brain Mapp 29: 848–857
Nioche C, Cabanis EA, Habas C (2009) Functional connectivity of the human red nucleus in the brain resting state at 3T. AJNR Am J Neuroradiol 30: 396–403
Margulies DS, Vincent JL, Kelly C, Lohmann G, Uddin LQ, Biswal BB, Villringer A, Castellanos FX, Milham MP, Petrides M (2009) Precuneus shares intrinsic functional architecture in humans and monkeys. Proc Natl Acad Sci USA 106: 20069–20074
van den Heuvel MP, Pol HEH (2010) Specific somatotopic organization of functional connections of the primary motor network during resting state. Hum Brain Mapp 31: 631–644
Fox MD, Corbetta M, Snyder AZ, Vincent JL, Raichle ME (2006) Spontaneous neuronal activity distinguishes human dorsal and ventral attention systems. Proc Natl Acad Sci USA 103: 10046–10051
Vincent JL, Snyder AZ, Fox MD, Shannon BJ, Andrews JR, Raichle ME, Buckner RL (2006) Coherent spontaneous activity identifies a hippocampal-parietal memory network. J Neurophysiol 96: 3517–3531
Vincent JL, Kahn I, Snyder AZ, Raichle ME, Buckner RL (2008) Evidence for a frontoparietal control system revealed by intrinsic functional connectivity. J Neurophysiol 100: 3328–3342
Vincent JL, Patel GH, Fox MD, Snyder AZ, Baker JT, Van Essen DC, Zempel JM, Snyder LH, Corbetta M, Raichle ME (2007) Intrinsic functional architecture in the anaesthetized monkey brain. Nature 447: 83–86
Vincent JL, Kahn I, Essen DCV, Buckner RL (2010) Functional connectivity of the macaque posterior parahippocampal cortex. J Neurophysiol 103: 793–800
Pawela CP, Biswal BB, Cho YR, Kao DS, Li R, Jones SR, Schulte ML, Matloub HS, Hudetz AG, Hyde JS (2008) Resting-state functional connectivity of the rat brain. Magn Reson Med 59: 1021–1029
Kannurpatti SS, Biswal BB, Kim YR, Rosen BR (2008) Spatio-temporal characteristics of low-frequency bold signal fluctuations in isoflurane-anesthetized rat brain. Neuroimage 40: 1738–1747
Shehzad Z, Kelly AMC, Reiss PT, Gee DG, Gotimer K, Uddin LQ, Lee SH, Margulies DS, Roy AK, Biswal BB, Petkova E, Castellanos FX, Milham MP (2009) The resting brain: unconstrained yet reliable. Cereb Cortex 19: 2209–2229
Dosenbach NUF, Fair DA, Miezin FM, Cohen AL, Wenger KK, Dosenbach RAT, Fox MD, Snyder AZ, Vincent JL, Raichle ME, Schlaggar BL, Petersen SE (2007) Distinct brain networks for adaptive and stable task control in humans. Proc Natl Acad Sci USA 104: 11073–11078
Kennedy DN, Lange N, Makris N, Bates J, Meyer J, Caviness VS (1998) Gyri of the human neocortex: an MRI-based analysis of volume and variance. Cereb Cortex 8: 372–384
Makris N, Meyer JW, Bates JF, Yeterian EH, Kennedy DN, Caviness VS (1999) MRI-based topographic parcellation of human cerebral white matter and nuclei II. rationale and applications with systematics of cerebral connectivity. Neuroimage 9: 18–45
Toro R, Fox PT, Paus T (2008) Functional coactivation map of the human brain. Cereb Cortex 18: 2553–2559
Kiviniemi V, Kantola JH, Jauhiainen J, Hyvrinen A, Tervonen O (2003) Independent component analysis of nondeterministic fMRI signal sources. Neuroimage 19: 253–260
van de Ven VG, Formisano E, Prvulovic D, Roeder CH, Linden DE (2004) Functional connectivity as revealed by spatial independent component analysis of fMRI measurements during rest. Hum Brain Mapp 22: 165–178
Beckmann CF, DeLuca M, Devlin JT, Smith SM (2005) Investigations into resting-state connectivity using independent component analysis. Philos Trans R Soc Lond B Biol Sci 360: 1001–1013
Damoiseaux JS, Rombouts SA, Barkhof F, Scheltens P, Stam CJ, Smith SM, Beckmann CF (2006) Consistent resting-state networks across healthy subjects. Proc Natl Acad Sci USA 103: 13848–13853
Himberg J, Hyvrinen A, Esposito F (2004) Validating the independent components of neuroimaging time series via clustering and visualization. Neuroimage 22: 1214–1222
Arfanakis K, Cordes D, Haughton VM, Moritz CH, Quigley MA, Meyerand ME (2000) Combining independent component analysis and correlation analysis to probe interregional connectivity in fMRI task activation datasets. Magn Reson Imaging 18: 921–930
Thomas CG, Harshman RA, Menon RS (2002) Noise reduction in bold-based fMRI using component analysis. Neuroimage 17: 1521–1537
Perlbarg V, Bellec P, Anton JL, Plgrini-Issac M, Doyon J, Benali H (2007) Corsica: correction of structured noise in fMRI by automatic identification of ICA components. Magn Reson Imaging 25: 35–46
Tohka J, Foerde K, Aron AR, Tom SM, Toga AW, Poldrack RA (2008) Automatic independent component labeling for artifact removal in fMRI. Neuroimage 39: 1227–1245
Starck T, Remes J, Nikkinen J, Tervonen O, Kiviniemi V (2010) Correction of low-frequency physiological noise from the resting state BOLD fMRI-effect on ICA default mode analysis at 1.5T. J Neurosci Methods 186: 179–185
Martino FD, Gentile F, Esposito F, Balsi M, Salle FD, Goebel R, Formisano E (2007) Classification of fMRI independent components using IC-fingerprints and support vector machine classifiers. Neuroimage 34: 177–194
Guo Y, Pagnoni G (2008) A unified framework for group independent component analysis for multi-subject fMRI data. Neuroimage 42: 1078–1093
Calhoun VD, Liu J, Adali T (2009) A review of group ICA for fMRI data and ICA for joint inference of imaging, genetic, and ERP data. Neuroimage 45: S163–S172
Greicius MD, Srivastava G, Reiss AL, Menon V (2004) Default-mode network activity distinguishes Alzheimer’s disease from healthy aging: evidence from functional MRI. Proc Natl Acad Sci USA 101: 4637–4642
Seeley WW, Crawford RK, Zhou J, Miller BL, Greicius MD (2009) Neurodegenerative diseases target large-scale human brain networks. Neuron 62: 42–52
Habas C, Kamdar N, Nguyen D, Prater K, Beckmann CF, Menon V, Greicius MD (2009) Distinct cerebellar contributions to intrinsic connectivity networks. J Neurosci 29: 8586–8594
Filippini N, MacIntosh BJ, Hough MG, Goodwin GM, Frisoni GB, Smith SM, Matthews PM, Beckmann CF, Mackay CE (2009) Distinct patterns of brain activity in young carriers of the APOe-epsilon4 allele. Proc Natl Acad Sci USA 106: 7209–7214
Beckmann CF, Mackay CE, Filippini N, Smith SM (2009) Group comparison of resting-state fMRI data using multi-subject ICA and dual regression. NeuroImage 47: S39–S41
Calhoun VD, Adali T, McGinty VB, Pekar JJ, Watson TD, Pearlson GD (2001) fMRI activation in a visual-perception task: network of areas detected using the general linear model and independent components analysis. Neuroimage 14: 1080–1088
Wang Z, Peterson BS (2008) Partner-matching for the automated identification of reproducible ICA components from fMRI datasets: algorithm and validation. Hum Brain Mapp 29: 875–893
De Luca M, Beckmann CF, De Stefano N, Matthews PM, Smith SM (2006) fMRI resting state networks define distinct modes of long-distance interactions in the human brain. Neuroimage 29: 1359–1367
Kiviniemi V, Starck T, Remes J, Long X, Nikkinen J, Haapea M, Veijola J, Moilanen I, Isohanni M, Zang YF, Tervonen O (2009) Functional segmentation of the brain cortex using high model order group PICA. Hum Brain Mapp 30: 3865–3886
Chen S, Ross TJ, Zhan W, Myers CS, Chuang KS, Heishman SJ, Stein EA, Yang Y (2008) Group independent component analysis reveals consistent resting-state networks across multiple sessions. Brain Res 1239: 141–151
Zuo XN, Kelly C, Adelstein JS, Klein DF, Castellanos FX, Milham MP (2010) Reliable intrinsic connectivity networks: test-retest evaluation using ICA and dual regression approach. Neuroimage 49: 2163–2177
Meindl T, Teipel S, Elmouden R, Mueller S, Koch W, Dietrich O, Coates U, Reiser M, Glaser C (2010) Test-retest reproducibility of the default-mode network in healthy individuals. Hum Brain Mapp 31: 237–246
Franco AR, Pritchard A, Calhoun VD, Mayer AR (2009) Interrater and intermethod reliability of default mode network selection. Hum Brain Mapp 30: 2293–2303
Fransson P, Skiőld B, Horsch S, Nordell A, Blennow M, Lagercrantz H, Aden U (2007) Resting-state networks in the infant brain. Proc Natl Acad Sci USA 104: 15531–15536
Sorg C, Riedl V, Muhlau M, Calhoun VD, Eichele T, Laer L, Drzezga A, Forstl H, Kurz A, Zimmer C, Wohlschlager AM (2007) Selective changes of resting-state networks in individuals at risk for Alzheimer’s disease. Proc Natl Acad Sci USA 104: 18760–18765
Qi Z, Wu X, Wang Z, Zhang N, Dong H, Yao L, Li K (2010) Impairment and compensation coexist in amnestic MCI default mode network. Neuroimage 50: 48–55
Greicius MD, Flores BH, Menon V, Glover GH, Solvason HB, Kenna H, Reiss AL, Schatzberg AF (2007) Resting-state functional connectivity in major depression: abnormally increased contributions from subgenual cingulate cortex and thalamus. Biol Psychiatry 62: 429–437
Jafri MJ, Pearlson GD, Stevens M, Calhoun VD (2008) A method for functional network connectivity among spatially independent resting-state components in schizophrenia. Neuroimage 39: 1666–1681
Wolf RC, Sambataro F, Vasic N, Schnfeldt-Lecuona C, Ecker D, Landwehrmeyer B (2008) Aberrant connectivity of lateral prefrontal networks in presymptomatic huntington’s disease. Exp Neurol 213: 137–144
Mohammadi B, Kollewe K, Samii A, Krampfl K, Dengler R, Münte TF (2009) Changes of resting state brain networks in amyotrophic lateral sclerosis. Exp Neurol 217: 147–153
Zhang Z, Lu G, Zhong Y, Tan Q, Yang Z, Liao W, Chen Z, Shi J, Liu Y (2009) Impaired attention network in temporal lobe epilepsy: a resting fMRI study. Neurosci Lett 458: 97–101
Vanhaudenhuyse A, Noirhomme Q, Tshibanda LJF, Bruno MAA, Boveroux P, Schnakers C, Soddu A, Perlbarg V, Ledoux D, Brichant JFF, Moonen G, Maquet P, Greicius MD, Laureys S, Boly M (2010) Default network connectivity reflects the level of consciousness in non-communicative brain-damaged patients. Brain 133: 161–171
Smith SM, Fox PT, Miller KL, Glahn DC, Fox PM, Mackay CE, Filippini N, Watkins KE, Toro R, Laird AR, Beckmann CF (2009) Correspondence of the brain’s functional architecture during activation and rest. Proc Natl Acad Sci USA 106: 13040–13045
Daubechies I, Roussos E, Takerkart S, Benharrosh M, Golden C, D’Ardenne K, Richter W, Cohen JD, Haxby J (2009) Independent component analysis for brain fMRI does not select for independence. Proc Natl Acad Sci USA 106: 10415–10422
van den Heuvel M, Mandl R, Hulshoff Pol H (2008) Normalized cut group clustering of resting-state fMRI data. PLoS One 3: e2001
Salvador R, Suckling J, Coleman MR, Pickard JD, Menon D, Bullmore E (2005) Neurophysiological architecture of functional magnetic resonance images of human brain. Cereb Cortex 15: 1332–1342
Cohen AL, Fair DA, Dosenbach NU, Miezin FM, Dierker D, Van Essen DC, Schlaggar BL, Petersen SE (2008) Defining functional areas in individual human brains using resting functional connectivity MRI. Neuroimage 41: 45–57
Craddock RC, Holtzheimer rPE, Hu XP, Mayberg HS (2009) Disease state prediction from resting state functional connectivity. Magn Reson Med 62: 1619–1628
Zhu CZ, Zang YF, Cao QJ, Yan CG, He Y, Jiang TZ, Sui MQ, Wang YF (2008) Fisher discriminative analysis of resting-state brain function for attention-deficit/hyperactivity disorder. Neuroimage 40: 110–120
Shen H, Wang L, Liu Y, Hu D (2010) Discriminative analysis of resting-state functional connectivity patterns of schizophrenia using low dimensional embedding of fMRI. Neuroimage 49: 3110–3121
Achard S, Bullmore E (2007) Efficiency and cost of economical brain functional networks. PLoS Comput Biol 3: e17
He Y, Wang J, Wang L, Chen ZJ, Yan C, Yang H, Tang H, Zhu C, Gong Q, Zang Y, Evans AC (2009) Uncovering intrinsic modular organization of spontaneous brain activity in humans. PLoS ONE 4: e5226
Zang Y, Jiang T, Lu Y, He Y, Tian L (2004) Regional homogeneity approach to fMRI data analysis. Neuroimage 22: 394–400
Zou QHH, Zhu CZZ, Yang Y, Zuo XNN, Long XYY, Cao QJJ, Wang YFF, Zang YFF (2008) An improved approach to detection of amplitude of low-frequency fluctuation (ALFF) for resting-state fMRI: fractional ALFF. J Neurosci Methods 172: 137–141
Beckmann M, Johansen-Berg H, Rushworth MF (2009) Connectivity-based parcellation of human cingulate cortex and its relation to functional specialization. J Neurosci 29: 1175–1190
Klein JC, Behrens TE, Robson MD, Mackay CE, Higham DJ, Johansen-Berg H (2007) Connectivity-based parcellation of human cortex using diffusion MRI: Establishing reproducibility, validity and observer independence in BA 44/45 and SMA/pre-SMA. Neuroimage 34: 204–211
Palomero-Gallagher N, Vogt BA, Schleicher A, Mayberg HS, Zilles K (2009) Receptor architecture of human cingulate cortex: evaluation of the four-region neurobiological model. Hum Brain Mapp 30: 2336–2355
Fischer H, Hennig J (1999) Neural network-based analysis of mr time series. Magn Reson Med 41: 124–131
Goutte C, Toft P, Rostrup E, Nielsen F, Hansen LK (1999) On clustering fmri time series. Neuroimage 9: 298–310
Wismüller A, Lange O, Dersch DR, Leinsinger GL, Hahn K, Pütz B, Auer D (2002) Cluster analysis of biomedical image time-series. Int J Comput Vis 46: 103–128
Bellec P, Rosa-Neto P, Lyttelton OC, Benali H, Evans AC (2010) Multi-level bootstrap analysis of stable clusters in resting-state fmri. Neuroimage 51: 1126–1139
Cordes D, Haughton V, Carew JD, Arfanakis K, Maravilla K (2002) Hierarchical clustering to measure connectivity in fMRI resting-state data. Magn Reson Imaging 20: 305–317
Mezer A, Yovel Y, Pasternak O, Gorfine T, Assaf Y (2009) Cluster analysis of resting-state fMRI time series. Neuroimage 45: 1117–1125
Wismüller A, Lange O, Auer D, Leinsinger G (2010) Model-free functional MRI analysis for detecting low-frequency functional connectivity in the human brains. Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series, March 2001, vol 7624, presented at the Society of Photo-Optical Instrumentation Engineers (SPIE) Conference
Thirion B, Dodel S, Poline JB (2006) Detection of signal synchronizations in resting-state fMRI datasets. Neuroimage 29: 321–327
Shi J, Malik J (2000) Normalized cuts and image segmentation. IEEE Trans Pattern Anal Mach Intell 22: 888–905
Norman KA, Polyn SM, Detre GJ, Haxby JV (2006) Beyond mind-reading: multi-voxel pattern analysis of fMRI data. Trends Cogn Sci 10: 424–430
Haynes JD, Rees G (2006) Decoding mental states from brain activity in humans. Nat Rev Neurosci 7: 523–534
Haxby JV, Gobbini MI, Furey ML, Ishai A, Schouten JL, Pietrini P (2001) Distributed and overlapping representations of faces and objects in ventral temporal cortex. Science 293: 2425–2430
Cox DD, Savoy RL (2003) Functional magnetic resonance imaging (fMRI) “brain reading”: detecting and classifying distributed patterns of fMRI activity in human visual cortex. Neuroimage 19: 261–270
Haynes JD, Rees G (2005) Predicting the orientation of invisible stimuli from activity in human primary visual cortex. Nat Neurosci 8: 686–691
Haynes JD, Sakai K, Rees G, Gilbert S, Frith C, Passingham RE (2007) Reading hidden intentions in the human brain. Curr Biol 17: 323–328
Kriegeskorte N, Goebel R, Bandettini P (2006) Information-based functional brain mapping. Proc Natl Acad Sci USA 103: 3863–3868
Polyn SM, Natu VS, Cohen JD, Norman KA (2005) Category-specific cortical activity precedes retrieval during memory search. Science 310: 1963–1966
Pereira F, Mitchell T, Botvinick M (2009) Machine learning classifiers and fMRI: a tutorial overview. Neuroimage 45: S199–S209
Mur M, Bandettini PA, Kriegeskorte N (2009) Revealing representational content with pattern-information fMRI—an introductory guide. Soc Cogn Affect Neurosci 4: 101–109
Hanke M, Halchenko YO, Sederberg PB, Hanson SJ, Haxby JV, Pollmann S (2009) PyMVPA: a python toolbox for multivariate pattern analysis of fMRI data. Neuroinformatics 7: 37–53
Guyon I, Elisseeff A (2003) An introduction to variable and feature selection. J Mach Learn Res 3: 1157–1182
Zhu CZ, Zang YF, Liang M, Tian LX, He Y, Li XB, Sui MQ, Wang YF, Jiang TZ (2005) Discriminative analysis of brain function at resting-state for attention-deficit/hyperactivity disorder. Med Image Comput Comput Assist Interv 8: 468–475
Wang K, Jiang T, Liang M, Wang L, Tian L, Zhang X, Li K, Liu Z (2006) Discriminative analysis of early Alzheimer’s disease based on two intrinsically anti-correlated networks with resting-state fMRI. Med Image Comput Comput Assist Interv 9: 340–347
Jafri MJ, Calhoun VD (2006) Functional classification of schizophrenia using feed forward neural networks. Conf Proc IEEE Eng Med Biol Soc (Suppl):6631–6634
Diestel R (2005) Graph theory, vol 173 of graduate texts in mathematics, 3rd edn. Springer
Bullmore E, Sporns O (2009) Complex brain networks: graph theoretical analysis of structural and functional systems. Nat Rev Neurosci 10: 186–198
Eguluz VM, Chialvo DR, Cecchi GA, Baliki M, Apkarian AV (2005) Scale-free brain functional networks. Phys Rev Lett 94: 018102
Nakamura T, Hillary FG, Biswal BB (2009) Resting network plasticity following brain injury. PLoS ONE 4: e8220
Achard S, Salvador R, Whitcher B, Suckling J, Bullmore E (2006) A resilient, low-frequency, small-world human brain functional network with highly connected association cortical hubs. J Neurosci 26: 63–72
Wang L, Zhu C, He Y, Zang Y, Cao Q, Zhang H, Zhong Q, Wang Y (2009) Altered small-world brain functional networks in children with attention-deficit/hyperactivity disorder. Hum Brain Mapp 30: 638–649
Buckner RL, Sepulcre J, Talukdar T, Krienen FM, Liu H, Hedden T, Andrews-Hanna JR, Sperling RA, Johnson KA (2009) Cortical hubs revealed by intrinsic functional connectivity: mapping, assessment of stability, and relation to Alzheimer’s disease. J Neurosci 29: 1860–1873
Lohmann G, Margulies DS, Horstmann A, Pleger B, Lepsien J, Goldhahn D, Schloegl H, Stumvoll M, Villringer A, Turner R (2010) Eigenvector centrality mapping for analyzing connectivity patterns in fmri data of the human brain. PLoS One 5: e10232
Stam CJ, Reijneveld JC (2007) Graph theoretical analysis of complex networks in the brain. Nonlinear Biomed Phys 1: 3
Shen X, Papademetris X, Constable RT (2010) Graph-theory based parcellation of functional subunits in the brain from resting-state fMRI data. Neuroimage 50: 1027–1035
Ferrarini L, Veer IM, Baerends E, van Tol MJJ, Renken RJ, van der Wee NJ, Veltman DJ, Aleman A, Zitman FG, Penninx BW, van Buchem MA, Reiber JH, Rombouts SA, Milles J (2009) Hierarchical functional modularity in the resting-state human brain. Hum Brain Mapp 30: 2220–2231
Soffer SN, Vázquez A (2005) Network clustering coefficient without degree-correlation biases. Phys Rev E 71: 057101
Sokal RR, Michener CD (1958) A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull 28: 1409–1438
Jiang B, Claramunt C (2004) Topological analysis of urban street networks. Environ Plann B Plann Des 31: 151–162
Amaral LAN, Scala A, Barth M, Stanley HE (2000) Classes of small-world networks. Proc Natl Acad Sci USA 97: 11149–11152
Nanavati AA, Gurumurthy S, Das G, Chakraborty D, Dasgupta K, Mukherjea S, Joshi A (2006) On the structural properties of massive telecom call graphs: findings and implications. In: CIKM ’06: Proceedings of the 15th ACM international conference on information and knowledge management, pp 435–444, ACM
Kogut B, Walker G (2001) The small world of germany and the durability of national networks. Am Sociol Rev 66: 317–335
Supekar K, Menon V, Rubin D, Musen M, Greicius MD (2008) Network analysis of intrinsic functional brain connectivity in Alzheimer’s disease. PLoS Comput Biol 4: e1000100
Hayasaka S, Laurienti PJ (2010) Comparison of characteristics between region-and voxel-based network analyses in resting-state fMRI data. NeuroImage 50: 499–508
Achard S, Bullmore E (2007) Efficiency and cost of economical brain functional networks. PLoS Comput Biol 3: e17
Wang J, Wang L, Zang Y, Yang H, Tang H, Gong Q, Chen Z, Zhu C, He Y (2009) Parcellation-dependent small-world brain functional networks: a resting-state fMRI study. Hum Brain Mapp 30: 1511–1523
Zang YFF, He Y, Zhu CZZ, Cao QJJ, Sui MQQ, Liang M, Tian LXX, Jiang TZZ, Wang YFF (2007) Altered baseline brain activity in children with ADHD revealed by resting-state functional MRI. Brain Dev 29: 83–91
Biswal B, Hudetz AG, Yetkin FZ, Haughton VM, Hyde JS (1997) Hypercapnia reversibly suppresses low-frequency fluctuations in the human motor cortex during rest using echo-planar MRI. J Cereb Blood Flow Metab 17: 301–308
Yang H, Long XYY, Yang Y, Yan H, Zhu CZZ, Zhou XPP, Zang YFF, Gong QYY (2007) Amplitude of low frequency fluctuation within visual areas revealed by resting-state functional MRI. Neuroimage 36: 144–152
Cao QJ, Zang YF, Wang YF (2007) Brain functions in attention deficit hyperactivity disorder combined and inattentive subtypes: a resting-state functional magnetic resonance imaging study. Beijing Da Xue Xue Bao 39: 261–265
Hoptman MJ, Zuo XNN, Butler PD, Javitt DC, D’Angelo D, Mauro CJ, Milham MP (2010) Amplitude of low-frequency oscillations in schizophrenia: a resting state fMRI study. Schizophr Res 117: 13–20
Long XYY, Zuo XNN, Kiviniemi V, Yang Y, Zou QHH, Zhu CZZ, Jiang TZZ, Yang H, Gong QYY, Wang L, Li KCC, Xie S, Zang YFF (2008) Default mode network as revealed with multiple methods for resting-state functional MRI analysis. J Neurosci Methods 171: 349–355
He Y, Zang Y, Jiang T, Liang M, Gong G (2004) Medical image computing and computer-assisted intervention MICCAI 2004. In: Barillot C, Haynor DR, Hellier P (eds) Detecting functional connectivity of the cerebellum using low frequency fluctuations (LFFs). Springer, Berlin, pp 907–915
Liu H, Liu Z, Liang M, Hao Y, Tan L, Kuang F, Yi Y, Xu L, Jiang T (2006) Decreased regional homogeneity in schizophrenia: a resting state functional magnetic resonance imaging study. Neuroreport 17: 19–22
Cao Q, Zang Y, Sun L, Sui M, Long X, Zou Q, Wang Y (2006) Abnormal neural activity in children with attention deficit hyperactivity disorder: a resting-state functional magnetic resonance imaging study. Neuroreport 17: 1033–1036
He Y, Wang L, Zang Y, Tian L, Zhang X, Li K, Jiang T (2007) Regional coherence changes in the early stages of Alzheimer’s disease: a combined structural and resting-state functional MRI study. Neuroimage 35: 488–500
Yuan Y, Zhang Z, Bai F, Yu H, Shi Y, Qian Y, Liu W, You J, Zhang X, Liu Z (2008) Abnormal neural activity in the patients with remitted geriatric depression: a resting-state functional magnetic resonance imaging study. J Affect Disord 111: 145–152
Wu T, Long X, Zang Y, Wang L, Hallett M, Li K, Chan P (2009) Regional homogeneity changes in patients with parkinson’s disease. Hum Brain Mapp 30: 1502–1510
Paakki JJ, Rahko J, Long XY, Moilanen I, Tervonen O, Nikkinen J, Starck T, Remes J, Tuula H, Haapsamo H, Jussila K, Kuusikko-Gauffin S, Mattila ML, Zang YF, Kiviniemi V (2010) Alterations in regional homogeneity of resting-state brain activity in autism spectrum disorders. Brain Res 1321: 169–179
Uddin LQ, Kelly AM, Biswal BB, Margulies DS, Shehzad Z, Shaw D, Ghaffari M, Rotrosen J, Adler LA, Castellanos FX, Milham MP (2008) Network homogeneity reveals decreased integrity of default-mode network in ADHD. J Neurosci Methods 169: 249–254
Biswal BB, Mennes M, Zuo XN, Gohel S, Kelly C, Smith SM, Beckmann CF, Adelstein JS, Buckner RL, Colcombe S, Dogonowski AM, Ernst M, Fair D, Hampson M, Hoptman MJ, Hyde JS, Kiviniemi VJ, Ktter R, Li SJ, Lin CP, Lowe MJ, Mackay C, Madden DJ, Madsen KH, Margulies DS, Mayberg HS, McMahon K, Monk CS, Mostofsky SH, Nagel BJ, Pekar JJ, Peltier SJ, Petersen SE, Riedl V, Rombouts SARB, Rypma B, Schlaggar BL, Schmidt S, Seidler RD, Siegle GJ, Sorg C, Teng GJ, Veijola J, Villringer A, Walter M, Wang L, Weng XC, Whitfield-Gabrieli S, Williamson P, Windischberger C, Zang YF, Zhang HY, Castellanos FX, Milham MP (2010) Toward discovery science of human brain function. Proc Natl Acad Sci USA 107: 4734–4739
Jiang T, He Y, Zang Y, Weng X (2004) Modulation of functional connectivity during the resting state and the motor task. Hum Brain Mapp 22: 63–71
Xiong J, Ma L, Wang B, Narayana S, Duff EP, Egan GF, Fox PT (2009) Long-term motor training induced changes in regional cerebral blood flow in both task and resting states. Neuroimage 45: 75–82
Harrison BJ, Pujol J, Ortiz H, Fornito A, Pantelis C, Yucel M (2008) Modulation of brain resting-state networks by sad mood induction. PLoS ONE 3: e1794
Albert NB, Robertson EM, Miall RC (2009) The resting human brain and motor learning. Curr Biol 19: 1023–1027
Mantini D, Perrucci MG, Del Gratta C, Romani GL, Corbetta M (2007) Electrophysiological signatures of resting state networks in the human brain. Proc Natl Acad Sci USA 104: 13170–13175
van den Heuvel MP, Mandl RC, Kahn RS, Hulshoff Pol HE (2009) Functionally linked resting-state networks reflect the underlying structural connectivity architecture of the human brain. Hum Brain Mapp 30: 3127–3141
Hagmann P, Cammoun L, Gigandet X, Meuli R, Honey CJ, Wedeen VJ, Sporns O (2008) Mapping the structural core of human cerebral cortex. PLoS Biol 6: e159
Honey CJ, Sporns O, Cammoun L, Gigandet X, Thiran JP, Meuli R, Hagmann P (2009) Predicting human resting-state functional connectivity from structural connectivity. Proc Natl Acad Sci USA 106: 2035–2040
Skudlarski P, Jagannathan K, Calhoun VD, Hampson M, Skudlarska BA, Pearlson G (2008) Measuring brain connectivity: diffusion tensor imaging validates resting state temporal correlations. Neuroimage 43: 554–561
Teipel SJ, Bokde ALW, Meindl T, Amaro E, Soldner J, Reiser MF, Herpertz SC, Mőller HJJ, Hampel H (2010) White matter microstructure underlying default mode network connectivity in the human brain. Neuroimage 49: 2021–2032