Supplementary References
Outline
Introduction

Intrinsic functional networks:
o Sensorimotor: (Biswal, Yetkin et al. 1995; Lowe, Mock et al. 1998; Xiong, Parsons et al.
1999; Cordes, Haughton et al. 2000; Kiviniemi, Jauhiainen et al. 2000)
o Visual: (Cordes, Haughton et al. 2000)
o Auditory: (Cordes, Haughton et al. 2000)
o Language: (Cordes, Haughton et al. 2000; Hampson, Peterson et al. 2002)
o Attention: (Fox, Snyder et al. 2005; Fox, Corbetta et al. 2006)
o Default mode: (Greicius, Krasnow et al. 2003; Fox, Snyder et al. 2005; Fransson 2005)
o Control: (Damoiseaux, Rombouts et al. 2006; Dosenbach, Fair et al. 2007; Seeley, Menon et
al. 2007; Vincent, Kahn et al. 2008)
o Thalamus: (Stein, Moritz et al. 2000; Anand, Li et al. 2005; Beckmann, DeLuca et al. 2005;
De Luca, Beckmann et al. 2006; Dosenbach, Fair et al. 2007; Greicius, Flores et al. 2007;
Seeley, Menon et al. 2007; Zhang, Snyder et al. 2008)
o basal ganglia: (Di Martino, Scheres et al. 2008)
o Limbic system: (Vincent, Snyder et al. 2006; Roy, Shehzad et al. 2009)
o Cerebellum: (Allen, McColl et al. 2005; Habas, Kamdar et al. 2009; Krienen and Buckner
2009; O'Reilly, Beckmann et al. 2009; Smith, Fox et al. 2009)

Coherent spontaneous activity across multiple states of consciousness and behavior:
o During task performance: (Arfanakis, Cordes et al. 2000; Greicius and Menon 2004; Fox,
Snyder et al. 2006; Fransson 2006)
o Wakeful rest: (Biswal, Yetkin et al. 1995; Lowe, Mock et al. 1998; Cordes, Haughton et al.
2000; Greicius, Krasnow et al. 2003; Beckmann, DeLuca et al. 2005; Fox, Snyder et al. 2005;
Fransson 2005)
o Sleep: (Horovitz, Fukunaga et al. 2008; Liu, Flax et al. 2008; Larson-Prior, Zempel et al.
2009)
o Loss of consciousness induced by anesthetics/sedatives: (Kiviniemi, Jauhiainen et al. 2000;
Fransson, Skiold et al. 2007; Greicius, Kiviniemi et al. 2008; Johnston, Vaishnavi et al. 2008;
Kiviniemi 2008)
o Across species under anesthesia: (Lu, Zuo et al. 2007; Vincent, Patel et al. 2007; Zhao,
Zhao et al. 2008; Moeller, Nallasamy et al. 2009)
Methodology
Functional connectivity mapping

Functional connectivity: (Horwitz 2003; Fingelkurts and Kahkonen 2005)

Cardiac, respiratory signal: (Glover, Li et al. 2000; De Luca, Beckmann et al. 2006; Shmueli, van
Gelderen et al. 2007; Birn, Murphy et al. 2008)

Independent Component Analysis (ICA): (Biswal and Ulmer 1999; Calhoun, Adali et al. 2001;
Kiviniemi, Kantola et al. 2003; van de Ven, Formisano et al. 2004)

“Optimal” number of independent components (ICs): (Cordes and Nandy 2006; Li, Adali et al.
2007)
 Post-processing IC identification: (Damoiseaux, Beckmann et al. 2008; Sui, Adali et al. 2009)
Spatial levels of neuronal synchrony

Partial correlation: (Cordes, Haughton et al. 2002; Sun, Miller et al. 2004; Salvador, Suckling et
al. 2005; Salvador, Martinez et al. 2007; van den Heuvel, Mandl et al. 2008)

Hierarchical clustering: (Cordes, Haughton et al. 2002; Ferrarini, Veer et al. 2009; Meunier,
Achard et al. 2009)
Graph theory
 Small world networks: (Bassett and Bullmore 2006; Sporns and Honey 2006)
Regional synchrony

Integrated local correlation: (Deshpande, LaConte et al. 2009)

Regional homogeneity and disease: (Zhu, Zang et al. 2005; Cao, Zang et al. 2006; Liu, Liu et al.
2006; He, Wang et al. 2007; Shi, Liu et al. 2007; Zhu, Zang et al. 2008)
Intrinsic brain activity and disease
Depression

Cortex-thalamus connectivity: (Ray and Price 1993)

Classification using vector support machines: (Craddock, Holtzheimer et al. 2009; Deshpande,
James et al. 2009)
Normal development and aging

Sensorimotor and visual functional networks early in life: (Lin, Zhu et al. 2008; Liu, Flax et al.
2008)

fcMRI changes into young adulthood: (Kelly, Di Martino et al. 2009)

Aging: (Achard and Bullmore 2007; Damoiseaux, Beckmann et al. 2008; Meunier, Achard et al.
2009)
Use of regionally confined measures

Regional homogeneity: (Zhu, Zang et al. 2005; Cao, Zang et al. 2006; Liu, Liu et al. 2006; He,
Wang et al. 2007; Shi, Liu et al. 2007; Zhu, Zang et al. 2008)
Neurosurgical application

Task-evoked fMRI clinical applications: (Haberg, Kvistad et al. 2004; Vlieger, Majoie et al. 2004)

fcMRI changes under deep anesthesia: (Peltier, Kerssens et al. 2005)

Language fcMRI: (Hampson, Tokoglu et al. 2006)
Correlates of intrinsic activity
Structural correlates.

Inhibitory neurotransmission: (Chatton, Pellerin et al. 2003)

Diffusion weighted imaging (DWI): (Hagmann, Jonasson et al. 2006; Mori, Oishi et al. 2009)

fcMRI and DWI: (Koch, Norris et al. 2002; Skudlarski, Jagannathan et al. 2008; van den Heuvel,
Mandl et al. 2009)
Electrophysiological correlates

Intrinsic activity observed with other imaging modalities: (Berger 1929; Bishop 1933; Llinas 1988;
Meister, Wong et al. 1991; Steriade, McCormick et al. 1993; Weliky and Katz 1999; Chiu and
Weliky 2001; Kenet, Bibitchkov et al. 2003; Buzsaki and Draguhn 2004; Fiser, Chiu et al. 2004;
Vanhatalo, Palva et al. 2004; Yuste, MacLean et al. 2005; Nir, Mukamel et al. 2008; White,
Snyder et al. 2009) (for an English translation of (Berger 1929), see (Gloor 1969))

Combined fcMRI and other imaging modalities: (Goldman, Stern et al. 2002; Laufs, Krakow et al.
2003; Moosmann, Ritter et al. 2003; Feige, Scheffler et al. 2005; Laufs, Lengler et al. 2006;
Laufs, Walker et al. 2007; Lu, Zuo et al. 2007; Mantini, Perrucci et al. 2007; He, Snyder et al.
2008; Scheeringa, Bastiaansen et al. 2008)

fcMRI spatiotemporal dynamics: (Majeed, Magnuson et al. 2009)
Conclusions

predicting and responding to future environmental events: (Knill and Pouget 2004; Behrens,
Woolrich et al. 2007; Fox and Raichle 2007)

Interaction of intrinsic activity with task: (Peltier, LaConte et al. 2005; Waites, Stanislavsky et al.
2005; Fransson 2006; Duff, Johnston et al. 2008; Barnes, Bullmore et al. 2009; Hasson,
Nusbaum et al. 2009; Xiong, Ma et al. 2009)

Correlations in band-limited power: (Bruns, Eckhorn et al. 2000)
Box 1

Freely available tools for fMRI and fcMRI analysis: (Friston, Holmes et al. 1994; Cox 1996;
Smith, Jenkinson et al. 2004; Calhoun, Liu et al. 2009)
Box 3

Task-evoked fMRI in predicting mental states: (Haxby, Gobbini et al. 2001; Haynes and Rees
2005; Kamitani and Tong 2005)

Classification algorithms:
o Discriminative analysis: (Wang, Jiang et al. 2006)
o Non-parametric density estimation: (Cacoullos 1966; 1989)
o Support vector machines: (Craddock, Holtzheimer et al. 2009; Deshpande, James et al.
2009)
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