Atlas-based analysis of resting-state functional connectivity: Evaluation for reproducibility and multi-modal anatomy-function correlation studies

NeuroImage

Volumn 61, Issue 3, 2012, Pages 613-621

  Faria, Andreia V ^a   Joel, Suresh E ^a,b   Zhang, Yajing ^a   Oishi, Kenichi ^a   van Zjil, Peter C M ^a,b   Miller, Michael I ^a   Pekar, James J ^a,b   Mori, Susumu ^a,b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b KENNEDY KRIEGER INSTITUTE   (United States)

Author keywords

Atlas; Connectivity; FMRI; Resting state; Rsfc fMRI

Indexed keywords

ADULT; ANATOMICAL CONCEPTS; ARTICLE; ATLAS BASED ANALYSIS; BRAIN FUNCTION; BRAIN MAPPING; BRAIN REGION; CONTROLLED STUDY; CORRELATION ANALYSIS; FEMALE; FUNCTIONAL MAGNETIC RESONANCE IMAGING; FUNCTIONAL MORPHOLOGY; HUMAN; HUMAN EXPERIMENT; IMAGE ANALYSIS; INTERNAL CONSISTENCY; MALE; MATHEMATICAL COMPUTING; NERVE CELL NETWORK; NEUROANATOMY; NORMAL HUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; RESTING STATE FUNCTIONAL CONNECTIVITY; SIGNAL NOISE RATIO; TEST RETEST RELIABILITY; TISSUE STRUCTURE; VOXEL BASED MORPHOMETRY;

ADULT; ALGORITHMS; ATLASES AS TOPIC; BRAIN; BRAIN MAPPING; DATA INTERPRETATION, STATISTICAL; FEMALE; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; LINEAR MODELS; MAGNETIC RESONANCE IMAGING; MALE; MIDDLE AGED; NEURAL PATHWAYS; REPRODUCIBILITY OF RESULTS; YOUNG ADULT;

EID: 84861191169     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2012.03.078     Document Type: Article

References (58)

1. Achard S., Salvador R., Whitcher B., Suckling J., Bullmore E. A resilient, low-frequency, small-world human brain functional network with highly connected association cortical hubs. J. Neurosci. 2006, 26(1):63-72.
2. Anderson J.S., Druzgal T.J., Lopez-Larson M., Jeong E.K., Desai K., Yurgelun-Todd D. Network anticorrelations, global regression, and phase-shifted soft tissue correction. Hum. Brain Mapp. 2011, 32(6):919-934.
3. Anderson J.S., Ferguson M.A., Lopez-Larson M., Yurgelun-Todd D. Reproducibility of single-subject functional connectivity measurements AJNR. Am. J. Neuroradiol. 2011, 32(3):548-555.
4. Behzadi Y., Restom K., Liau J., Liu T.T. A component based noise correction method (CompCor) for BOLD and perfusion based fMRI. NeuroImage 2007, 37(1):90-101.
5. Biswal B., Yetkin F.Z., Haughton V.M., Hyde J.S. Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magn. Reson. Med. 1995, 34(4):537-541.
6. Buckwalter J.A., Parvizi J., Morecraft R.J., van Hoesen G.W. Thalamic projections to the posteromedial cortex in the macaque. J. Comp. Neurol. 2008, 507(5):1709-1733.
7. Bullmore E., Sporns O. Complex brain networks: graph theoretical analysis of structural and functional systems Nature Reviews. Neuroscience 2009, 10(3):186-198.
8. Calhoun V.D., Adali T., Pearlson G.D., Pekar J.J. A method for making group inferences from functional MRI data using independent component analysis. Hum. Brain Mapp. 2001, 14(3):140-151.
9. Calhoun V.D., Adali T., Pearlson G.D., Pekar J.J. Spatial and temporal independent component analysis of functional MRI data containing a pair of task-related waveforms. Hum. Brain Mapp. 2001, 13(1):43-53.
10. Ceritoglu C., Oishi K., Li X., Chou M.C., Younes L., Albert M., Lyketsos C., van Zijl P.C., Miller M.I., Mori S. Multi-contrast large deformation diffeomorphic metric mapping for diffusion tensor imaging. NeuroImage 2009, 47(2):618-627.
11. Colby C.L., Gattass R., Olson C.R., Gross C.G. Topographical organization of cortical afferents to extrastriate visual area PO in the macaque: a dual tracer study. J. Comp. Neurol. 1988, 269(3):392-413.
12. Corbetta M., Shulman G.L. Control of goal-directed and stimulus-driven attention in the brain Nature Reviews. Neuroscience 2002, 3(3):201-215.
13. Craddock R.C., James G.A., Holtzheimer P.E., Hu X.P., Mayberg H.S. A whole brain fMRI atlas generated via spatially constrained spectral clustering. Hum. Brain Mapp. 2011, (Jul 18, Electronic publication ahead of print). doi:10.1002/hbm.21333.
14. Damoiseaux J.S., Rombouts S.A., Barkhof F., Scheltens P., Stam C.J., Smith S.M., Beckmann C.F. Consistent resting-state networks across healthy subjects. Proc. Natl. Acad. Sci. U. S. A. 2006, 103(37):13848-13853.
15. De Luca M., Beckmann C.F., De Stefano N., Matthews P.M., Smith S.M. fMRI resting state networks define distinct modes of long-distance interactions in the human brain. NeuroImage 2006, 29(4):1359-1367.
16. Eickhoff S.B., Stephan K.E., Mohlberg H., Grefkes C., Fink G.R., Amunts K., Zilles K. A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data. NeuroImage 2005, 25(4):1325-1335.
17. Faria A.V., Zhang J., Oishi K., Li X., Jiang H., Akhter K., Hermoye L., Lee S.K., Hoon A., Stachinko E., et al. Atlas-based analysis of neurodevelopment from infancy to adulthood using diffusion tensor imaging and applications for automated abnormality detection. NeuroImage 2010, 52(2):415-428.
18. Faria A.V., Hoon A., Stashinko E., Li X., Jiang H., Mashayekh A., Akhter K., Hsu J., Oishi K., Zhang J., et al. Quantitative analysis of brain pathology based on MRI and brain atlases-applications for cerebral palsy. NeuroImage 2011, 54(3):1854-1861.
19. Fox M.D., Snyder A.Z., Vincent J.L., Corbetta M., Van Essen D.C., Raichle M.E. The human brain is intrinsically organized into dynamic, anticorrelated functional networks. Proc. Natl. Acad. Sci. U. S. A. 2005, 102(27):9673-9678.
20. Fox M.D., Corbetta M., Snyder A.Z., Vincent J.L., Raichle M.E. Spontaneous neuronal activity distinguishes human dorsal and ventral attention systems. Proc. Natl. Acad. Sci. U. S. A. 2006, 103(26):10046-10051.
21. Fransson P. How default is the default mode of brain function? Further evidence from intrinsic BOLD signal fluctuations. Neuropsychologia 2006, 44(14):2836-2845.
22. Glover G.H., Li T.Q., Ress D. Image-based method for retrospective correction of physiological motion effects in fMRI: RETROICOR. Magn. Reson. Med. 2000, 44(1):162-167.
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. U. S. A. 2003, 100(1):253-258.
24. Greicius M.D., Srivastava G., Reiss A.L., Menon V. Default-mode network activity distinguishes Alzheimer's disease from healthy aging: evidence from functional MRI. Proc. Natl. Acad. Sci. U. S. A. 2004, 101(13):4637-4642.
25. Hagmann P., Cammoun L., Gigandet X., Meuli R., Honey C.J., Wedeen V.J., Sporns O. Mapping the structural core of human cerebral cortex. PLoS Biol. 2008, 6(7):e159.
26. Hampson M., Peterson B.S., Skudlarski P., Gatenby J.C., Gore J.C. Detection of functional connectivity using temporal correlations in MR images. Hum. Brain Mapp. 2002, 15(4):247-262.
27. Hampson M., Olson I.R., Leung H.C., Skudlarski P., Gore J.C. Changes in functional connectivity of human MT/V5 with visual motion input. Neuroreport 2004, 15(8):1315-1319.
28. He Y., Wang J., Wang L., Chen Z.J., Yan C., Yang H., Tang H., Zhu C., Gong Q., Zang Y., et al. Uncovering intrinsic modular organization of spontaneous brain activity in humans. PLoS One 2009, 4(4). e5226.
29. Honey C.J., Kotter R., Breakspear M., Sporns O. Network structure of cerebral cortex shapes functional connectivity on multiple time scales. Proc. Natl. Acad. Sci. U. S. A. 2007, 104(24):10240-10245.
30. Honey C.J., Sporns O., Cammoun L., Gigandet X., Thiran J.P., Meuli R., Hagmann P. Predicting human resting-state functional connectivity from structural connectivity. Proc. Natl. Acad. Sci. U. S. A. 2009, 106(6):2035-2040.
31. Lancaster J.L., Woldorff M.G., Parsons L.M., Liotti M., Freitas C.S., Rainey L., Kochunov P.V., Nickerson D., Mikiten S.A., Fox P.T. Automated Talairach atlas labels for functional brain mapping. Hum. Brain Mapp. 2000, 10(3):120-131.
32. Landman B.A., Huang A.J., Gifford A., Vikram D.S., Lim I.A., Farrell J.A., Bogovic J.A., Hua J., Chen M., Jarso S., et al. Multi-parametric neuroimaging reproducibility: a 3-T resource study. NeuroImage 2011, 54(4):2854-2866.
33. Leichnetz G.R. Connections of the medial posterior parietal cortex (area 7m) in the monkey. Anat. Rec. 2001, 263(2):215-236.
34. Lin P., Hasson U., Jovicich J., Robinson S. A neuronal basis for task-negative responses in the human brain. Cereb. Cortex 2011, 21(4):821-830.
35. Lowe M.J., Mock B.J., Sorenson J.A. Functional connectivity in single and multislice echoplanar imaging using resting-state fluctuations. NeuroImage 1998, 7(2):119-132.
36. Luo C., Li Q., Lai Y., Xia Y., Qin Y., Liao W., Li S., Zhou D., Yao D., Gong Q. Altered functional connectivity in default mode network in absence epilepsy: a resting-state fMRI study. Hum. Brain Mapp. 2011, 32(3):438-449.
37. Maldjian J.A., Laurienti P.J., Kraft R.A., Burdette J.H. An automated method for neuroanatomic and cytoarchitectonic atlas-based interrogation of fMRI data sets. NeuroImage 2003, 19(3):1233-1239.
38. Mars R.B., Sallet J., Schuffelgen U., Jbabdi S., Toni I., Rushworth M.F. Connectivity-based subdivisions of the human right "temporoparietal junction area": evidence for different areas participating in different cortical networks. Cereb. Cortex 2011, (Sep 27, Electronic publication ahead of print).
39. 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.
40. Miller M.I., Beg M.F., Ceritoglu C., Stark C. Increasing the power of functional maps of the medial temporal lobe by using large deformation diffeomorphic metric mapping. Proc. Natl. Acad. Sci. U. S. A. 2005, 102(27):9685-9690.
41. Morecraft R.J., Cipolloni P.B., Stilwell-Morecraft K.S., Gedney M.T., Pandya D.N. Cytoarchitecture and cortical connections of the posterior cingulate and adjacent somatosensory fields in the rhesus monkey. J. Comp. Neurol. 2004, 469(1):37-69.
42. Mori S., Oishi K., Jiang H., Jiang L., Li X., Akhter K., Hua K., Faria A.V., Mahmood A., Woods R., et al. Stereotaxic white matter atlas based on diffusion tensor imaging in an ICBM template. NeuroImage 2008, 40(2):570-582.
43. Oishi K., Zilles K., Amunts K., Faria A., Jiang H., Li X., Akhter K., Hua K., Woods R., Toga A.W., et al. Human brain white matter atlas: identification and assignment of common anatomical structures in superficial white matter. NeuroImage 2008, 43(3):447-457.
44. Oishi K., Faria A., Jiang H., Li X., Akhter K., Zhang J., Hsu J.T., Miller M.I., van Zijl P.C., Albert M., et al. Atlas-based whole brain white matter analysis using large deformation diffeomorphic metric mapping: application to normal elderly and Alzheimer's disease participants. NeuroImage 2009, 46(2):486-499.
45. Pandya D.N., Seltzer B. Intrinsic connections and architectonics of posterior parietal cortex in the rhesus monkey. J. Comp. Neurol. 1982, 204(2):196-210.
46. Seeley W.W., Crawford R.K., Zhou J., Miller B.L., Greicius M.D. Neurodegenerative diseases target large-scale human brain networks. Neuron 2009, 62(1):42-52.
47. 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., et al. The resting brain: unconstrained yet reliable. Cereb. Cortex 2009, 19(10):2209-2229.
48. Sheline Y.I., Price J.L., Yan Z., Mintun M.A. Resting-state functional MRI in depression unmasks increased connectivity between networks via the dorsal nexus. Proc. Natl. Acad. Sci. U. S. A. 2010, 107(24):11020-11025.
49. Smith S.M., Fox P.T., Miller K.L., Glahn D.C., Fox P.M., Mackay C.E., Filippini N., Watkins K.E., Toro R., Laird A.R., et al. Correspondence of the brain's functional architecture during activation and rest. Proc. Natl. Acad. Sci. U. S. A. 2009, 106(31):13040-13045.
50. Song M., Du H., Wu N., Hou B., Wu G., Wang J., Feng H., Jiang T. Impaired resting-state functional integrations within default mode network of generalized tonic-clonic seizures epilepsy. PloS One 2011, 6(2):e17294.
51. Tzourio-Mazoyer N., Landeau B., Papathanassiou D., Crivello F., Etard O., Delcroix N., Mazoyer B., Joliot M. Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. NeuroImage 2002, 15(1):273-289.
52. van de Ven V.G., Formisano E., Prvulovic D., Roeder C.H., Linden D.E. Functional connectivity as revealed by spatial independent component analysis of fMRI measurements during rest. Hum. Brain Mapp. 2004, 22(3):165-178.
53. Wang J., Wang L., Zang Y., Yang H., Tang H., Gong Q., Chen Z., Zhu C., He Y. Parcellation-dependent small-world brain functional networks: a resting-state fMRI study. Hum. Brain Mapp. 2009, 30(5):1511-1523.
54. Wang J.H., Zuo X.N., Gohel S., Milham M.P., Biswal B.B., He Y. Graph theoretical analysis of functional brain networks: test-retest evaluation on short- and long-term resting-state functional MRI data. PloS One 2011, 6(7):e21976.
55. Woods R.P., Grafton S.T., Holmes C.J., Cherry S.R., Mazziotta J.C. Automated image registration: I. General methods and intrasubject, intramodality validation. J. Comput. Assist. Tomogr. 1998, 22(1):139-152.
56. Zhang S., Li C.S. Functional connectivity mapping of the human precuneus by resting state fMRI. NeuroImage 2012, 59(4):3548-3562.
57. Zhang Y., Zhang J., Oishi K., Faria A.V., Jiang H., Li X., Akhter K., Rosa-Neto P., Pike B., Evans A., et al. Atlas-guided tract reconstruction for automated and comprehensive examination of the white matter anatomy. NeuroImage 2010, 52(4):1289-1301.
58. Zuo X.N., Kelly C., Adelstein J.S., Klein D.F., Castellanos F.X., Milham M.P. Reliable intrinsic connectivity networks: test-retest evaluation using ICA and dual regression approach. NeuroImage 2010, 49(3):2163-2177.