Hand classification of fMRI ICA noise components

NeuroImage

Volumn 154, Issue , 2017, Pages 188-205

  Griffanti, Ludovica ^a   Douaud, Gwenaëlle ^a   Bijsterbosch, Janine ^a   Evangelisti, Stefania ^a,b   Alfaro Almagro, Fidel ^a   Glasser, Matthew F ^c   Duff, Eugene P ^a   Fitzgibbon, Sean ^a   Westphal, Robert ^d   Carone, Davide ^a,e   Beckmann, Christian F ^a,f   Smith, Stephen M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF BOLOGNA   (Italy)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e UNIVERSITY OF MILANO BICOCCA   (Italy)

^f RADBOUD UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLASSIFICATION; FUNCTIONAL MAGNETIC RESONANCE IMAGING; HUMAN; INDEPENDENT COMPONENT ANALYSIS; INFORMATION PROCESSING; NOISE; NOISE REDUCTION; NONHUMAN; PRACTICE GUIDELINE; PRIORITY JOURNAL; SIGNAL PROCESSING; ADULT; BRAIN; CHILD; DIAGNOSTIC IMAGING; FUNCTIONAL NEUROIMAGING; IMAGE PROCESSING; NUCLEAR MAGNETIC RESONANCE IMAGING; PROCEDURES;

ADULT; BRAIN; CHILD; FUNCTIONAL NEUROIMAGING; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MAGNETIC RESONANCE IMAGING;

EID: 85008185859     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2016.12.036     Document Type: Article

References (64)

1. Allen, E.A., Erhardt, E.B., Damaraju, E., Gruner, W., Segall, J.M., Silva, R.F., Havlicek, M., Rachakonda, S., Fries, J., Kalyanam, R., Michael, A.M., Caprihan, A., Turner, J.A., Eichele, T., Adelsheim, S., Bryan, A.D., Bustillo, J., Clark, V.P., Feldstein Ewing, S.W., Filbey, F., Ford, C.C., Hutchison, K., Jung, R.E., Kiehl, K.A., Kodituwakku, P., Komesu, Y.M., Mayer, A.R., Pearlson, G.D., Phillips, J.P., Sadek, J.R., Stevens, M., Teuscher, U., Thoma, R.J., Calhoun, V.D., A baseline for the multivariate comparison of resting-state networks. Front. Syst. Neurosci., 5, 2011, 2.
2. Beall, E.B., Lowe, M.J., Isolating physiologic noise sources with independently determined spatial measures. Neuroimage 37 (2007), 1286–1300.
3. Beckmann, C.F., Modelling with independent components. Neuroimage 62 (2012), 891–901.
4. Beckmann, C.F., DeLuca, M., Devlin, J.T., Smith, S.M., Investigations into resting-state connectivity using independent component analysis. Philos. Trans. R. Soc. Lond. B Biol. Sci. 360 (2005), 1001–1013.
5. Beckmann, C.F., Smith, S.M., Probabilistic independent component analysis for functional magnetic resonance imaging. IEEE Trans. Med. Imaging 23 (2004), 137–152.
6. Bhaganagarapu, K., Jackson, G.D., Abbott, D.F., An automated method for identifying artifact in independent component analysis of resting-state FMRI. Front. Hum. Neurosci., 7, 2013, 343.
7. Bijsterbosch, J., Smith, S., Forster, S., John, O.P., Bishop, S.J., Resting state correlates of subdimensions of anxious affect. J. Cogn. Neurosci. 26 (2014), 914–926.
8. Calhoun, V.D., Adali, T., Stevens, M.C., Kiehl, K.A., Pekar, J.J., Semi-blind ICA of fMRI: a method for utilizing hypothesis-derived time courses in a spatial ICA analysis. Neuroimage 25 (2005), 527–538.
9. Calhoun, V.D., Kiehl, K.A., Pearlson, G.D., Modulation of temporally coherent brain networks estimated using ICA at rest and during cognitive tasks. Hum. Brain Mapp. 29 (2008), 828–838.
10. Chen, J.E., Glover, G.H., BOLD fractional contribution to resting-state functional connectivity above 0.1 Hz. Neuroimage 107 (2015), 207–218.
11. 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 29 (2006), 1359–1367.
12. 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 34 (2007), 177–194.
13. Demertzi, A., Gomez, F., Crone, J.S., Vanhaudenhuyse, A., Tshibanda, L., Noirhomme, Q., Thonnard, M., Charland-Verville, V., Kirsch, M., Laureys, S., Soddu, A., Multiple fMRI system-level baseline connectivity is disrupted in patients with consciousness alterations. Cortex 52 (2014), 35–46.
14. Doria, V., Beckmann, C.F., Arichi, T., Merchant, N., Groppo, M., Turkheimer, F.E., Counsell, S.J., Murgasova, M., Aljabar, P., Nunes, R.G., Larkman, D.J., Rees, G., Edwards, A.D., Emergence of resting state networks in the preterm human brain. Proc. Natl. Acad. Sci. USA 107 (2010), 20015–20020.
15. Du, Y., Allen, E.A., He, H., Sui, J., Wu, L., Calhoun, V.D., Artifact removal in the context of group ICA: a comparison of single-subject and group approaches. Hum. Brain Mapp. 37 (2016), 1005–1025.
16. Erberich, S.G., Friedlich, P., Seri, I., Nelson, M.D. Jr., Bluml, S., Functional MRI in neonates using neonatal head coil and MR compatible incubator. Neuroimage 20 (2003), 683–692.
17. Feinberg, D.A., Yacoub, E., The rapid development of high speed, resolution and precision in fMRI. Neuroimage 62 (2012), 720–725.
18. Feis, R.A., Smith, S.M., Filippini, N., Douaud, G., Dopper, E.G., Heise, V., Trachtenberg, A.J., van Swieten, J.C., van Buchem, M.A., Rombouts, S.A., Mackay, C.E., ICA-based artifact removal diminishes scan site differences in multi-center resting-state fMRI. Front. Neurosci., 9, 2015, 395.
19. Filippini, N., MacIntosh, B.J., Hough, M.G., Goodwin, G.M., Frisoni, G.B., Smith, S.M., Matthews, P.M., Beckmann, C.F., Mackay, C.E., Distinct patterns of brain activity in young carriers of the APOE-epsilon4 allele. Proc. Natl. Acad. Sci. USA 106 (2009), 7209–7214.
20. 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., Consortium, W.U.-M.H., The minimal preprocessing pipelines for the human connectome project. Neuroimage 80 (2013), 105–124.
21. Glasser, M.F.C., Coalson, T.S., Robinson, E.C., Hacker, C.D., Harwell, J., Yacoub, E., Ugurbil, K., Andersson, J., Beckmann, C.F., Jenkinson, M., Smith, S.M., Van Essen, D.C., A multi-modal parcellation of human cerebral cortex. Nature 536 (2016), 171–178.
22. Golestani, A.M., Chang, C., Kwinta, J.B., Khatamian, Y.B., Jean Chen, J., Mapping the end-tidal CO2 response function in the resting-state BOLD fMRI signal: spatial specificity, test-retest reliability and effect of fMRI sampling rate. Neuroimage 104 (2015), 266–277.
23. Gozzi, A., Schwarz, A.J., Large-scale functional connectivity networks in the rodent brain. Neuroimage 127 (2016), 496–509.
24. Griffanti, L., Dipasquale, O., Lagana, M.M., Nemni, R., Clerici, M., Smith, S.M., Baselli, G., Baglio, F., Effective artifact removal in resting state fMRI data improves detection of DMN functional connectivity alteration in Alzheimer's disease. Front. Hum. Neurosci., 9, 2015, 449.
25. Griffanti, L., Salimi-Khorshidi, G., Beckmann, C.F., Auerbach, E.J., Douaud, G., Sexton, C.E., Zsoldos, E., Ebmeier, K.P., Filippini, N., Mackay, C.E., Moeller, S., Xu, J., Yacoub, E., Baselli, G., Ugurbil, K., Miller, K.L., Smith, S.M., ICA-based artefact removal and accelerated fMRI acquisition for improved resting state network imaging. Neuroimage 95 (2014), 232–247.
26. Guldenmund, P., Gantner, I.S., Baquero, K., Das, T., Demertzi, A., Boveroux, P., Bonhomme, V., Vanhaudenhuyse, A., Bruno, M.A., Gosseries, O., Noirhomme, Q., Kirsch, M., Boly, M., Owen, A.M., Laureys, S., Gomez, F., Soddu, A., Propofol-induced frontal cortex disconnection: a study of resting-state networks, total brain connectivity, and mean bold signal oscillation frequencies. Brain Connect. 6 (2016), 225–237.
27. Hartendorp, M.O., Van der Stigchel, S., Wagemans, J., Klugkist, I., Postma, A., The activation of alternative response candidates: when do doubts kick in?. Acta Psychol. 139 (2012), 38–45.
28. Hyvarinen, A., Fast and robust fixed-point algorithms for independent component analysis. IEEE Trans. Neural Netw. 10 (1999), 626–634.
29. Jezzard, P., Clare, S., Sources of distortion in functional MRI data. Hum. Brain Mapp. 8 (1999), 80–85.
30. Kelly, R.E. Jr., Alexopoulos, G.S., Wang, Z., Gunning, F.M., Murphy, C.F., Morimoto, S.S., Kanellopoulos, D., Jia, Z., Lim, K.O., Hoptman, M.J., Visual inspection of independent components: defining a procedure for artifact removal from fMRI data. J. Neurosci. Methods 189 (2010), 233–245.
31. Kochiyama, T., Morita, T., Okada, T., Yonekura, Y., Matsumura, M., Sadato, N., Removing the effects of task-related motion using independent-component analysis. Neuroimage 25 (2005), 802–814.
32. Kullmann, S., Pape, A.A., Heni, M., Ketterer, C., Schick, F., Haring, H.U., Fritsche, A., Preissl, H., Veit, R., Functional network connectivity underlying food processing: disturbed salience and visual processing in overweight and obese adults. Cereb. Cortex 23 (2013), 1247–1256.
33. Kundu, P., Inati, S.J., Evans, J.W., Luh, W.M., Bandettini, P.A., Differentiating BOLD and non-BOLD signals in fMRI time series using multi-echo EPI. Neuroimage 60 (2012), 1759–1770.
34. Lang, J., Koth, R., Reiss, G., [On the origin, course and influx-vessels of the V. basalis and the V. cerebri interna (author's transl)]. Anat. Anz. 150 (1981), 385–423.
35. Lowe, M.J., Mock, B.J., Sorenson, J.A., Functional connectivity in single and multislice echoplanar imaging using resting-state fluctuations. Neuroimage 7 (1998), 119–132.
36. Mattiaccio, L.M., Coman, I.L., Schreiner, M.J., Antshel, K.M., Fremont, W.P., Bearden, C.E., Kates, W.R., Atypical functional connectivity in resting-state networks of individuals with 22q11.2 deletion syndrome: associations with neurocognitive and psychiatric functioning. J. Neurodev. Disord., 8, 2016, 2.
37. 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. 6 (1998), 160–188.
38. Moeller, S., Yacoub, E., Olman, C.A., Auerbach, E., Strupp, J., Harel, N., Ugurbil, K., Multiband multislice GE-EPI at 7 T, with 16-fold acceleration using partial parallel imaging with application to high spatial and temporal whole-brain fMRI. Magn. Reson. Med. 63 (2010), 1144–1153.
39. Moritz, C.H., Rogers, B.P., Meyerand, M.E., Power spectrum ranked independent component analysis of a periodic fMRI complex motor paradigm. Hum. Brain Mapp. 18 (2003), 111–122.
40. Murphy, G.L., Ross, B.H., Uncertainty in category-based induction: when do people integrate across categories?. J. Exp. Psychol. Learn Mem. Cogn. 36 (2010), 263–276.
41. Murphy, K., Birn, R.M., Bandettini, P.A., Resting-state fMRI confounds and cleanup. Neuroimage 80 (2013), 349–359.
42. Niazy, R.K., Xie, J., Miller, K., Beckmann, C.F., Smith, S.M., Spectral characteristics of resting state networks. Prog. Brain Res 193 (2011), 259–276.
43. Ohkawa, M., Fujiwara, N., Katoh, T., Mori, Y., Nakano, S., Tanabe, M., Honjo, Y., Nagao, S., Detection of subependymal veins using high-resolution magnetic resonance venography. Acta Med. Okayama 51 (1997), 321–325.
44. Olafsson, V., Kundu, P., Wong, E.C., Bandettini, P.A., Liu, T.T., Enhanced identification of BOLD-like components with multi-echo simultaneous multi-slice (MESMS) fMRI and multi-echo ICA. Neuroimage 112 (2015), 43–51.
45. Perlbarg, V., Bellec, P., Anton, J.L., Pelegrini-Issac, M., Doyon, J., Benali, H., CORSICA: correction of structured noise in fMRI by automatic identification of ICA components. Magn. Reson. Imaging 25 (2007), 35–46.
46. 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 59 (2012), 2142–2154.
47. Power, J.D., Schlaggar, B.L., Petersen, S.E., Recent progress and outstanding issues in motion correction in resting state fMRI. Neuroimage 105 (2015), 536–551.
48. Pruim, R.H., Mennes, M., Buitelaar, J.K., Beckmann, C.F., Evaluation of ICA-AROMA and alternative strategies for motion artifact removal in resting state fMRI. Neuroimage 112 (2015), 278–287.
49. Pruim, R.H., Mennes, M., van Rooij, D., Llera, A., Buitelaar, J.K., Beckmann, C.F., ICA-AROMA: a robust ICA-based strategy for removing motion artifacts from fMRI data. Neuroimage 112 (2015), 267–277.
50. Rodionov, R., De Martino, F., Laufs, H., Carmichael, D.W., Formisano, E., Walker, M., Duncan, J.S., Lemieux, L., Independent component analysis of interictal fMRI in focal epilepsy: comparison with general linear model-based EEG-correlated fMRI. Neuroimage 38 (2007), 488–500.
51. Rummel, C., Verma, R.K., Schopf, V., Abela, E., Hauf, M., Berruecos, J.F., Wiest, R., Time course based artifact identification for independent components of resting-state FMRI. Front. Hum. Neurosci., 7, 2013, 214.
52. Saad, Z.S., Gotts, S.J., Murphy, K., Chen, G., Jo, H.J., Martin, A., Cox, R.W., Trouble at rest: how correlation patterns and group differences become distorted after global signal regression. Brain Connect. 2 (2012), 25–32.
53. Salimi-Khorshidi, G., Douaud, G., Beckmann, C.F., Glasser, M.F., Griffanti, L., Smith, S.M., Automatic denoising of functional MRI data: combining independent component analysis and hierarchical fusion of classifiers. Neuroimage 90 (2014), 449–468.
54. Smith, S.M., Beckmann, C.F., Andersson, J., Auerbach, E.J., Bijsterbosch, J., Douaud, G., Duff, E., Feinberg, D.A., Griffanti, L., Harms, M.P., Kelly, M., Laumann, T., Miller, K.L., Moeller, S., Petersen, S., Power, J., Salimi-Khorshidi, G., Snyder, A.Z., Vu, A.T., Woolrich, M.W., Xu, J., Yacoub, E., Ugurbil, K., Van Essen, D.C., Glasser, M.F., Resting-state fMRI in the human connectome project. Neuroimage 80 (2013), 144–168.
55. Sochat, V., Supekar, K., Bustillo, J., Calhoun, V., Turner, J.A., Rubin, D.L., A robust classifier to distinguish noise from fMRI independent components. PLoS One, 9, 2014, e95493.
56. Soddu, A., Vanhaudenhuyse, A., Demertzi, A., Bruno, M.A., Tshibanda, L., Di, H., Melanie, B., Papa, M., Laureys, S., Noirhomme, Q., Resting state activity in patients with disorders of consciousness. Funct. Neurol. 26 (2011), 37–43.
57. Soros, P., Hachinski, V., Cardiovascular and neurological causes of sudden death after ischaemic stroke. Lancet Neurol. 11 (2012), 179–188.
58. Storti, S.F., Formaggio, E., Nordio, R., Manganotti, P., Fiaschi, A., Bertoldo, A., Toffolo, G.M., Automatic selection of resting-state networks with functional magnetic resonance imaging. Front. Neurosci., 7, 2013, 72.
59. Sui, J., Adali, T., Pearlson, G.D., Calhoun, V.D., An ICA-based method for the identification of optimal FMRI features and components using combined group-discriminative techniques. Neuroimage 46 (2009), 73–86.
60. Thomas, C.G., Harshman, R.A., Menon, R.S., Noise reduction in BOLD-based fMRI using component analysis. Neuroimage 17 (2002), 1521–1537.
61. 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 39 (2008), 1227–1245.
62. Toulmin, H., Beckmann, C.F., O'Muircheartaigh, J., Ball, G., Nongena, P., Makropoulos, A., Ederies, A., Counsell, S.J., Kennea, N., Arichi, T., Tusor, N., Rutherford, M.A., Azzopardi, D., Gonzalez-Cinca, N., Hajnal, J.V., Edwards, A.D., Specialization and integration of functional thalamocortical connectivity in the human infant. Proc. Natl. Acad. Sci. USA 112 (2015), 6485–6490.
63. Vergara, V.M., Mayer, A.R., Damaraju, E., Hutchison, K., Calhoun, V.D., The effect of preprocessing pipelines in subject classification and detection of abnormal resting state functional network connectivity using group ICA. Neuroimage, 2016.
64. Zerbi, V., Grandjean, J., Rudin, M., Wenderoth, N., Mapping the mouse brain with rs-fMRI: an optimized pipeline for functional network identification. Neuroimage 123 (2015), 11–21.