Resting-state fMRI in the Human Connectome Project

NeuroImage

Volumn 80, Issue , 2013, Pages 144-168

  Smith, Stephen M ^a   Beckmann, Christian F ^c,d   Andersson, Jesper ^a   Auerbach, Edward J ^b   Bijsterbosch, Janine ^a   Douaud, Gwenaëlle ^a   Duff, Eugene ^a   Feinberg, David A ^e   Griffanti, Ludovica ^a,f   Harms, Michael P ^g   Kelly, Michael ^a   Laumann, Timothy ^g   Miller, Karla L ^a   Moeller, Steen ^b   Petersen, Steve ^g   Power, Jonathan ^g   Salimi Khorshidi, Gholamreza ^a   Snyder, Abraham Z ^g   Vu, An T ^b,e   Woolrich, Mark W ^a   Xu, Junqian ^b,h   Yacoub, Essa ^b   Uǧurbil, Kamil ^b   Van Essen, David C ^g   Glasser, Matthew F ^g   more..

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^c RADBOUD UNIVERSITY   (Netherlands)

^d MIRA Institute for Biomedical Technology and Technical Medicine   (Netherlands)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f POLITECNICO DI MILANO   (Italy)

^g WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; ARTIFACT REDUCTION; BRAIN MAPPING; BRAIN REGION; COHORT ANALYSIS; CONNECTOME; ECHO PLANAR IMAGING; FUNCTIONAL MAGNETIC RESONANCE IMAGING; HUMAN; IMAGE ANALYSIS; IMAGE DISPLAY; IMAGE PROCESSING; IN VIVO STUDY; NEUROIMAGING; NORMAL HUMAN; PRIORITY JOURNAL; QUALITY CONTROL; RESTING STATE NETWORK; SIGNAL NOISE RATIO; VOLUNTEER;

BRAIN; CONNECTOME; HUMANS; MAGNETIC RESONANCE IMAGING; MODELS, ANATOMIC; MODELS, NEUROLOGICAL; NERVE NET; REST;

EID: 84880325951     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2013.05.039     Document Type: Article

References (68)

1. Beckmann C., Smith S. Probabilistic independent component analysis for functional magnetic resonance imaging. IEEE Trans. Med. Imaging 2004, 23(2):137-152.
2. Biswal B., Yetkin F., Haughton V.M., Hyde J. Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magn. Reson. Med. 1995, 34:537-541.
3. Blumensath T., Jbabdi S., Glasser M., Van Essen D., Ugurbil K., Behrens T., Smith S. Spatially constrained hierarchical parcellation of the brain with resting-state FMRI. Neuroimage 2013, 76:313-324.
4. Boxerman J.L., Bandettini P.A., Kwong K.K., Baker J.R., Davis T.L., Rosen B.R., Weisskoff R.M. The intravascular contribution to FMRI signal change: Monte Carlo modeling and diffusion-weighted studies in vivo. Magn. Reson. Med. 1995, 34(1):4-10.
5. Breuer F.A., Blaimer M., Heidemann R.M., Mueller M.F., Griswold M.A., Jakob P.M. Controlled aliasing in parallel imaging results in higher acceleration (CAIPIRINHA) for multi-slice imaging. Magn. Reson. Med. 2005, 53(3):684-691.
6. Cohen A., Fair D., Dosenbach N., Miezin F., Dierker D., Van Essen D., Schlaggar B., Petersen S. Defining functional areas in individual human brains using resting functional connectivity MRI. Neuroimage 2008, 41(1):45-57.
7. Craddock R., James G., Holtzheimer P., Hu X., Mayberg H. A whole brain fMRI atlas generated via spatially constrained spectral clustering. Hum. Brain Mapp. 2011, 33(8):1914-1928.
8. De Luca M., Beckmann C., De Stefano N., Matthews P., Smith S. FMRI resting state networks define distinct modes of long-distance interactions in the human brain. Neuroimage 2005, 29(4):1359-1367.
9. De Martino F., Gentile F., Esposito F., Balsi M., Di Salle F., Goebel R., Formisano E. Classification of fMRI independent components using IC-fingerprints and support vector machine classifiers. Neuroimage 2007, 34(1):177-194.
10. de Reus M.A., van den Heuvel M.P. The parcellation-based connectome: Limitations and extensions. Neuroimage 2013, 80:397-404.
11. Feinberg D., Reese T., Wedeen V. Simultaneous echo refocusing in EPI. Magn. Reson. Med. 2002, 48(1):1-5.
12. Feinberg D., Moeller S., Smith S., Auerbach E., Ramanna S., Glasser M., Miller K., Ugurbil K., Yacoub E. Multiplexed echo planar imaging for sub-second whole brain FMRI and fast diffusion imaging. PLoS One 2010, 5(12):e15710.
13. Filippini N., MacIntosh B., Hough M., Goodwin G., Frisoni G., Smith S., Matthews P., Beckmann C., Mackay C. Distinct patterns of brain activity in young carriers of the APOE-e4 allele. Proc. Natl. Acad. Sci. U. S. A. (PNAS) 2009, 106:7209-7214.
14. Flandin G., Kherif F., Pennec X., Rivi'ere D., Ayache N., Poline J.-B. Parcellation of brain images with anatomical and functional constraints for fMRI data analysis. Proceedings, IEEE International Symposium on Biomedical Imaging 2002, 907-910.
15. Fox M.D., Raichle M.E. Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nat. Rev. Neurosci. 2007, 8(9):700-711.
16. Fox M., Snyder A., Vincent J., Corbetta M., Van Essen D., Raichle M. The human brain is intrinsically organized into dynamic, anticorrelated functional networks. Proc. Natl. Acad. Sci. U. S. A. 2005, 102(27):9673-9678.
17. Fox M., Zhang D., Snyder A., Raichle M. The global signal and observed anticorrelated resting state brain networks. J. Neurophysiol. 2009, 101(6):3270-3283.
18. Friston K. Functional and effective connectivity: a review. Brain Connect. 2011, 1(1):13-36.
19. Friston K.J., Harrison L., Penny W. Dynamic causal modelling. Neuroimage 2003, 19(3):1273-1302.
20. Glasser M.F., Van Essen D.C. Mapping human cortical areas in vivo based on myelin content as revealed by T1-and T2-weighted MRI. J. Neurosci. 2011, 31(32):11597-11616.
21. Glasser M., Laumann T., Coalson T., Cohen A., Snyder A., Schlaggar B., Petersen S., Van Essen D. Comparison of surface gradients derived from myelin maps and functional connectivity analysis. Int. Conf. on Functional Mapping of the Human Brain 2011.
22. Glasser M.F., Sotiropoulos S.N., Wilson J.A., Coalson T.S., Fischl B., Andersson J.L., Xu J., Jbabdi S., Webster M., Polimeni J.R., Van Essen D.C., Jenkinson M. The minimal preprocessing pipelines for the Human Connectome Project. Neuroimage 2013, 80:105-124. - for the WU-Minn HCP Consortium.
23. Greicius M.D., Krasnow B., Reiss A.L., Menon V. Functional connectivity in the resting brain: a network analysis of the default mode hypothesis. Proc. Natl. Acad. Sci. 2003, 100(1):253-258.
24. Griffanti L., Salimi-Khorshidi G., Beckmann C.F., Bijsterbisch J., Auerbach E.J., Douaud G., Zsoldos E., Ebmeier K.P., Filippini N., Mackay C., Moeller S., Xu J., Yacoub E., Baselli G., Ugurbil K., Miller K.L., Smith S.M. Automated artefact removal and accelerated fMRI acquisition for improved Resting State Network imaging 2013, (in preparation).
25. He H., Liu T.T. A geometric view of global signal confounds in resting-state functional MRI. Neuroimage 2012, 59(3):2339-2348.
26. Kiviniemi V., Kantola J.-H., Jauhiainen J., Hyvr̈ arinen A., Tervonen O. Independent component analysis of nondeterministic fMRI signal sources. Neuroimage 2003, 19:253-260.
27. Larkman D.J., Hajnal J.V., Herlihy A.H., Coutts G.A., Young I.R., Ehnholm G. Use of multicoil arrays for separation of signal from multiple slices simultaneously excited. J. Magn. Reson. Imaging 2001, 13(2):313-317.
28. Mansfield P. Multi-planar image formation using NMR spin echoes. J. Phys. C Solid State Phys. 1977, 10(3):L55-L58.
29. Markov N., Ercsey-Ravasz M., Gomes A.R., Lamy C., Magrou L., Vezoli J., Misery P., Falchier A., Quilodran R., Gariel M., Sallet J., Gamanut R., Huissoud C., Clavagnier S., Giroud P., Sappey-Marinier D., Barone P., Dehay C., Toroczkai Z., Knoblauch K., Van Essen D., Kennedy H. A weighted and directed interareal connectivity matrix for macaque cerebral cortex. Cereb. Cortex 2013, (in press).
30. Marrelec G., Krainik A., Duffau H., Ṕeĺegrini-Issac M., Leh́ericy S., Doyon J., Benali H. Partial correlation for functional brain interactivity investigation in functional MRI. Neuroimage 2006, 32:228-237.
31. McKeown M.J., Makeig S., Brown G.G., Jung T.P., Kindermann S.S., Bell A.J., Sejnowski T.J. Analysis of fMRI data by blind separation into independent spatial components. Hum. Brain Mapp. 1998, 6(3):160-188.
32. Moeller S., Yacoub E., Olman C.A., Auerbach E., Strupp J., Harel N., Ugurbil K.C. Multiband multislice GE-EPI at 7Tesla, with 16-fold acceleration using partial parallel imaging with application to high spatial and temporal whole-brain fMRI. Magn. Reson. Med. 2010, 63(5):1144-1153.
33. Moeller S., Xu J., Auerbach E.J., Yacoub E., Ugurbil K. Signal leakage (L-factor) as a measure for parallel imaging performance among simultaneously multi-slice (SMS) excited and acquired signals. Proc ISMRM 2012, 519.
34. Murphy K., Birn R.M., Handwerker D.A., Jones T.B., Bandettini P.A. The impact of global signal regression on resting state correlations: are anti-correlated networks introduced?. Neuroimage 2009, 44(3):893-905.
35. Niazy R., Xie J., Miller K., Beckmann C., Smith S. Spectral characteristics of resting state networks. Progress in Brain Research 2011, vol. 193:259-276. Elsevier. E. Van Someren (Ed.).
36. Nunes R., Hajnal J., Golay X., Larkman D. Simultaneous slice excitation and reconstruction for single shot EPI. ISMRM 14th Annual Meeting 2006, 293.
37. Ogawa S., Lee T., Kay A., Tank D. Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Proc. Natl. Acad. Sci. 1990, 87(24):9868-9872.
38. Ogawa S., Menon R., Tank D., Kim S., Merkle H., Ellermann J., Ugurbil K. Functional brain mapping by blood oxygenation level-dependent contrast magnetic resonance imaging. A comparison of signal characteristics with a biophysical model. Biophys. J. 1993, 64(3):803-812.
39. Parkes L.M., Schwarzbach J.V., Bouts A.A., Pullens P., Kerskens C.M., Norris D.G. Quantifying the spatial resolution of the gradient echo and spin echo BOLD response at 3Tesla. Magn. Reson. Med. 2005, 54(6):1465-1472.
40. Perlbarg V., Bellec P., Anton J.-L., Ṕeĺegrini-Issac M., Doyon J., Benali H. CORSICA: correction of structured noise in fMRI by automatic identification of ICA components. Magn. Reson. Imaging 2007, 25(1):35-46.
41. Power J.D., Barnes K.A., Snyder A.Z., Schlaggar B.L., Petersen S.E. Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion. Neuroimage 2011, 59(3):2142-2154.
42. Rahmer J., Börnert P., Groen J., Bos C. Three-dimensional radial ultrashort echo-time imaging with T2 adapted sampling. Magn. Reson. Med. 2006, 55(5):1075-1082.
43. Robinson E., Jbabdi S., Andersson J., Smith S., Glasser M., Van Essen D., Burgess G., Harms M., Barch D., Jenkinson M. Multimodal surface matching: fast and generalisable cortical registration using discrete optimisation. Proc Information Processing in Medical Imaging 2013, Springer.
44. Satterthwaite T.D., Elliott M.A., Gerraty R.T., Ruparel K., Loughead J., Calkins M.E., Eickhoff S.B., Hakonarson H., Gur R.C., Gur R.E., Wolf D.H. An improved framework for confound regression and filtering for control of motion artifact in the preprocessing of resting-state functional connectivity data. Neuroimage 2013, 64(0):240-256.
45. Salimi-Khorshidi G., Douaud G., Beckmann C.F., Bijsterbisch J., Duff E., Glasser M.F., Griffanti L., Smith S.M. Automatic Denoising of Functional MRI Data: Combining Independent Component Analysis and Hierarchical Fusion of Classifiers 2013, (in preparation).
46. Setsompop K., Gagoski B.A., Polimeni J.R., Witzel T., Wedeen V.J., Wald L.L. Blipped-controlled aliasing in parallel imaging for simultaneous multislice echo planer imaging with reduced g-factor penalty. Magn. Reson. Med. 2012, 67(5):1210-1224.
47. Shmuel A., Yacoub E., Chaimow D., Logothetis N.K., Ugurbil K. Spatio-temporal point-spread function of fMRI signal in human gray matter at 7Tesla. Neuroimage 2007, 35(2):539-552.
48. Smith S. The future of FMRI connectivity. Neuroimage 2012, 62:1257-1266.
49. Smith S., Fox P., Miller K., Glahn D., Fox P., Mackay C., Filippini N., Watkins K., Toro R., Laird A., Beckmann C. Correspondence of the brain's functional architecture during activation and rest. Proc. Natl. Acad. Sci. U. S. A. (PNAS) 2009, 106(31):13040-13045.
50. Smith S., Miller K., Salimi-Khorshidi G., Webster M., Beckmann C., Nichols T., Ramsey J., Woolrich M. Network modelling methods for FMRI. Neuroimage 2011, 54:875-891.
51. Smith S., Miller K., Moeller S., Xu J., Auerbach E., Woolrich M., Beckmann C., Jenkinson M., Andersson J., Glasser M., Van Essen D., Feinberg D., Yacoub E., Ugurbil K. Temporally-independent functional modes of spontaneous brain activity. Proc. Natl. Acad. Sci. U. S. A. (PNAS) 2012, 109(8):3131-3136.
52. Smith, S., Miller, K., Varoquaux, G., Beckmann, C., Group-PCA for very large fMRI datasets. (in preparation).
53. Sotiropoulos S.N., Jbabdi S., Xu J., Andersson J.L., Moeller S., Auerbach E.J., Glasser M.F., Hernandez M., Sapiro G., Jenkinson M., Feinberg D.A., Yacoub E., Lenglet C., Van Essen D.C., Ugurbil K., Behrens T.E.J. Advances in diffusion MRI acquisition and processing in the Human Connectome Project. Neuroimage 2013, 80:125-143. - for the WU-Minn HCP Consortium.
54. Sporns O., Tononi G., Kötter R. The human connectome: a structural description of the human brain. PLoS Comput. Biol. 2005, 1(4):245-251.
55. Tohka J., Foerde K., Aron A.R., Tom S.M., Toga A.W., Poldrack R.A. Automatic independent component labeling for artifact removal in fMRI. Neuroimage 2008, 39(3):1227-1245.
56. Ugurbil K., Xu J., Auerbach E.J., Moeller S., Vu A.T., Duarte-Carvajalino J.M., Lenglet C., Wu X., Schmitter S., Van de Moortele P.F., Strupp J., Sapiro G., De Martino F., Wang D., Harel N., Garwood M., Chen L., Feinberg D.A., Smith S.M., Miller K.L., Sotiropoulos S.N., Jbabdi S., Andersson J.L.R., Behrens T.E.J., Glasser M.F., Van Essen D.C., Yacoub E. Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project. Neuroimage 2013, 80:80-104. - for the WU-Minn HCP Consortium.
57. Uludaǧ K., Müller-Bierl B., Uǧurbil K. An integrative model for neuronal activity-induced signal changes for gradient and spin echo functional imaging. Neuroimage 2009, 48(1):150-165.
58. van den Heuvel M., Hulshoff Pol H. Specific somatotopic organization of functional connections of the primary motor network during resting state. Hum. Brain Mapp. 2010, 31(4):631-644.
59. Van Dijk K.R., Hedden T., Venkataraman A., Evans K.C., Lazar S.W., Buckner R.L. Intrinsic functional connectivity as a tool for human connectomics: theory, properties, and optimization. J. Neurophysiol. 2010, 103(1):297-321.
60. Van Essen D., Glasser M., Dierker D., Harwell J., Coalson T. Parcellations and hemispheric asymmetries of human cerebral cortex analyzed on surface-based atalses. Cereb. Cortex 2012, 22:2241-2262.
61. Van Essen D.C., Smith S.M., Barch D.M., Behrens T.E.J., Yacoub E., Ugurbil K. The WU-Minn Human Connectome Project: An overview. Neuroimage 2013, 80:62-79. - for the WU-Minn HCP Consortium.
62. Varoquaux G., Gramfort A., Pedregosa F., Michel V., Thirion B. Multi-subject dictionary learning to segment an atlas of brain spontaneous activity. Proc Information Processing in Medical Imaging 2011, 562-573. Springer.
63. Vaughan J.T., Garwood M., Collins C., Liu W., DelaBarre L., Adriany G., Andersen P., Merkle H., Goebel R., Smith M., Ugurbil K. 7T vs. 4T: RF power, homogeneity, and signal-to-noise comparison in head images. Magn. Reson. Med. 2001, 46(1):24-30.
64. Wansapura J.P., Holland S.K., Dunn R.S., Ball W.S. NMR relaxation times in the human brain at 3.0Tesla. J. Magn. Reson. Imaging 1999, 9(4):531-538.
65. Wong E.C., Cox R.W., Song A.W. Optimized isotropic diffusion weighting. Magn. Reson. Med. 1995, 34(2):139-143.
66. Woolrich M., Ripley B., Brady J., Smith S. Temporal autocorrelation in univariate linear modelling of FMRI data. Neuroimage 2001, 14(6):1370-1386.
67. Xu J., Moeller S., Strupp J., Auerbach E., Chen L., Feinberg D., Ugurbil K., Yacoub E. Highly accelerated whole brain imaging using aligned-blipped-controlled aliasing multiband EPI. Proc ISMRM 2012, 2306.
68. Yacoub E., Shmuel A., Pfeuffer J., De Moortele V., Adriany G., Andersen P., Vaughan J.T., Merkle H., Ugurbil K., Hu X. Imaging brain function in humans at 7Tesla. Magn. Reson. Med. 2001, 45(4):588-594.