Physiological noise in brainstem fMRI

Frontiers in Human Neuroscience

Volumn , Issue OCT, 2013, Pages

  Brooks, Jonathan C W ^a   Faull, Olivia K ^b   Pattinson, Kyle T S ^b   Jenkinson, Mark ^b  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

7T; Brainstem; fMRI; Imaging; Physiological noise

Indexed keywords

ARTICLE; BRAIN STEM; BREATHING PATTERN; FUNCTIONAL MAGNETIC RESONANCE IMAGING; HEART CYCLE; HUMAN; INDEPENDENT COMPONENT ANALYSIS; MEASUREMENT; NOISE; PHYSIOLOGICAL NOISE; SIGNAL PROCESSING; STATISTICAL MODEL; TIME SERIES ANALYSIS;

EID: 84886392150     PISSN: 16625161     EISSN: None     Source Type: Journal    
DOI: 10.3389/fnhum.2013.00623     Document Type: Article

References (59)

1. Aja-Fernandez, S., Tristan-Vega, A., and Hoge, W. S. (2011). Statistical noise analysis in GRAPPA using a parametrized noncentral Chi approximation model. Magn. Reson. Med. 65, 1195-1206. doi:10.1002/mrm.22701
2. Beckmann, C. F., and Smith, S. M. (2004). Probabilistic independent component analysis for functional magnetic resonance imaging. IEEE Trans. Med. Imaging 23, 137-152. doi:10.1109/TMI.2003.822821
3. Beissner, F., Baudrexel, S., Volz, S., and Deichmann, R. (2010). Dual-echo EPI for non-equilibrium fMRI - implications of different echo combinations and masking procedures. Neuroimage 52, 524-531. doi:10. 1016/j.neuroimage.2010.04.243
4. Beissner, F., Deichmann, R., and Baudrexel S. (2011). fMRI of the brainstem using dual-echo EPI. Neuroimage 55, 1593-1599. doi:10.1016/j. neuroimage.2011.01.042
5. Birn, R. M., Diamond, J. B., Smith, M. A., and Bandettini, P. A. (2006). Separating respiratory-variation- related fluctuations from neuronal- activity-related fluctuations in fMRI. Neuroimage 31, 1536-1548. doi:10.1016/j.neuroimage.2006.02. 048
6. Breuer, F. A., Kannengiesser, S. A., Blaimer, M., Seiberlich, N., Jakob, P. A., and Griswold, M. A. (2009). General formulation for quantitative g-factor calculation in GRAPPA reconstructions. Magn. Reson. Med. 62, 739-746. doi:10.1002/mrm. 22066
7. Brooks, J. C. W., Beckmann, C. F., Miller, K. L., Wise, R. G., Porro, C. A., Tracey, I., et al. (2008). Physiological noise modelling for spinal functional magnetic resonance imaging studies. Neuroimage 39, 680-692. doi:10.1016/j.neuroimage.2007.09.018
8. Chang, C., Cunningham, J. P., and Glover, G. H. (2009). Influence of heart rate on the BOLD signal: the cardiac response function. Neuroimage 44, 857-869. doi:10.1016/j. neuroimage.2008.09.029
9. Churchill, N. W., Yourganov, G., Spring, R., Rasmussen, P. M., Lee, W., Ween, J. E., et al. (2012). PHYCAA: data-driven measurement and removal of physiological noise in BOLD fMRI. Neuroimage 59, 1299-1314. doi:10.1016/j.neuroimage.2011.08.021
10. Dagli, M. S., Ingeholm, J. E., and Haxby, J. V. (1999). Localization of cardiac-induced signal change in fMRI. Neuroimage 9, 407-415. doi:10.1006/nimg.1998.0424
11. de Zwart, J. A., Gelderen, P. V., Fukunaga, M., and Duyn, J. H.(2008). Reducing correlated noise in fMRI data. Magn. Reson. Med. 59, 939-945. doi:10.1002/mrm.21507
12. Deckers, R. H. R., van Gelderen, P., Ries, M., Barret, O., Duyn, J. H., Ikonomidou, V. N., et al. (2006). An adaptive filter for suppression of cardiac and respiratory noise in MRI time series data. Neuroimage 33, 1072-1081. doi: 10.1016/j. neuroimage.2006.08.006
13. Feinberg, D. A., Moeller, S., Smith, S. M., Auerbach, E., Ramanna, S., Glasser, M. F., et al. (2010). Multiplexed echo planar imaging for sub-second whole brain FMRI and fast diffusion imaging. PLoS ONE 5:15710. doi:10.1371/journal.pone.0015710
14. Frank, L. R., Buxton, R. B., and Wong, E. (2001).Estimation of respiration- induced noise fluctuations from undersampled multislice fMRI data. Magn. Reson. Med. 45, 635-644. doi: 10.1002/mrm.1086
15. Glover, G. H., Li, T. Q., and Ress, D. (2000). Image-based method for retrospective correction of physiological motion effects in fMRI: RETROICOR. Magn. Reson. Med. 44, 162-167. doi:10.1002/1522-2594(200007)44: 1<162::AID-MRM23>3.3.CO;2-5
16. Greitz, D., Franck, A., and Nordell B. (1993). On the pulsatile nature of intracranial and spinal CSF- circulation demonstrated by MR imaging. Acta Radiol. 34, 321-328. doi:10.3109/02841859309173251
17. Guimaraes, A. R., Melcher, J. R., Talavage, T. M., Baker, J. R., Ledden, P., Rosen, B. R., et al. (1998). Imaging subcortical auditory activity in humans. Hum. Brain Mapp. 6, 33-41. doi:10.1002/(SICI)1097- 0193(1998)6:1<33::AID-HBM3>3. 0.CO;2-M
18. Harvey, A. K., Pattinson, K. T. S., Brooks, J. C. W., Mayhew, S. D., Jenkinson, M., and Wise, R. G. (2008). Brainstem functional magnetic resonance imaging: disentangling signal from physiological noise. J. Magn. Reson. Imaging 28, 1337-1344. doi: 10.1002/jmri.21623
19. Hayen, A., Herigstad, M., Kelly, M., Okell, T. W., Murphy, K., Wise, R. G., et al. (2012). The effects of altered intrathoracic pressure on resting cerebral blood flow and its response to visual stimulation. Neuroimage 66, 479-488. doi: 10.1016/j.neuroimage.2012.10.049
20. Hu, X., Le, T. H., Parrish, T., and Erhard, P. (1995). Retrospective estimation and correction of physiological fluctuation in functional MRI. Magn. Reson. Med. 34, 201-212. doi:10. 1002/mrm.1910340211
21. Hutton, C., Josephs, O., Stadler, J., Featherstone, E., Reid, A., Speck, O., et al. (2011). The impact of physiological noise correction on fMRI at 7 T. Neuroimage 57, 101-112. doi:10.1016/j. neuroimage.2011.04.018
22. Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., and Smith, S. M. (2012). FSL. Neuroimage 62, 782-790. doi:10.1016/j. neuroimage.2011.09.015
23. Jezzard, P. (1999). "Physiological noise: strategies for correction, in Functional MRI, eds C. Moonen and P. A. Bandettini (Heidelberg: Springer- Verlag), 171-179.
24. Jezzard, P., Matthews, P. M., and Smith, S. M. (2003). Functional MRI. Oxford: Oxford University Press.
25. Josephs, O., Howseman, A., and Friston, K. (1997). Physiological noise modelling for multi-slice EPI fMRI using SPM. Proceedings of the 5th Annual MeetingofISMRM, Vancouver, 1682.
26. Klose, U., Strik, C., Kiefer, C., and Grodd, W. (2000). Detection of a relation between respiration and CSF pulsation with an echoplanar technique. J. Magn. Reson. Imaging 11, 438-444. doi:10.1002/(SICI) 1522-2586(200004)11:4<438::AID- JMRI12>3.0.CO;2-O
27. Kong, J., Kaptchuk, T. J., Polich, G., Kirsch, I., Vangel, M., Zyloney, C., et al. (2009). An fMRI study on the interaction and dissociation between expectation of pain relief and acupuncture treatment. Neuroimage 47,1066-1076. doi:10.1016/ j.neuroimage.2009.05.087
28. Kong, Y., Jenkinson, M., Andersson, J., Tracey, I., and Brooks, J. C. W. (2012). Assessment of physiological noise modelling methods for functional imaging of the spinal cord. Neuroimage 60, 1538-1549. doi:10.1016/j.neuroimage.2011.11.077
29. Kruger, G., and Glover, G. H. (2001). Physiological noise in oxygenation- sensitive magnetic resonance imaging. Magn. Reson. Med. 46, 631-637. doi:10.1002/mrm.1240
30. Kundu, P., Inati, S. J., Evans, J. W., Luh, W.-M., and Bandettini, P. A. (2012). Differentiating BOLD and non-BOLD signals in fMRI time series using multi-echo EPI. Neuroimage 60, 1759-1770. doi:10.1016/j.neuroimage.2011.12.028
31. Lin, T. (1999). "Physiology of the circulation, in Fundamentals of Anaesthesia, eds C. Pinnock, T. Lin, and T. Smith (London: Greenwich Medical Media), 331-360.
32. Macefield, V. G., and Henderson, L. A. (2010). Real-time imaging of the medullary circuitry involved in the generation of spontaneous muscle sympathetic nerve activity in awake subjects. Hum. Brain Mapp. 31, 539-549. doi:10.1002/hbm.20885
33. Malinen, S., Schurmann, M., Hlushchuk, Y., Forss, N., and Hari, R. (2006). Improved differentiation of tactile activations in human secondary somatosensory cortex and thalamus using cardiac- triggered fMRI. Exp. Brain Res. 174, 297-303. doi:10.1007/s00221-006- 0465-z
34. Murphy, K., Bodurka, J., and Bandettini, P. A. (2007). How long to scan? The relationship between fMRI temporal signal to noise ratio and necessary scan duration. Neuroimage 34, 565-574. doi:10.1016/j.neuroimage.2006.09.032
35. Parrish, T. B., Gitelman, D. R., LaBar, K. S., and Mesulam, M. M. (2000). Impact of signal- to-noise on functional MRI. Magn. Reson. Med. 44, 925-932. doi:10.1002/1522-2594(200012)44: 6<925::AID-MRM14>3.0.CO;2-M
36. Pattinson, K. T., Mitsis, G. D., Harvey, A. K., Jbabdi, S., Dirckx, S., Mayhew, S. D., et al. (2009a). Determination of the human brainstem respiratory control network and its cortical connections in vivo using functional and structural imaging. Neuroimage 44, 295-305. doi:10.1016/j.neuroimage. 2008.09.007
37. Pattinson, K. T. S., Governo, R. J., MacIntosh, B. J., Russell, E. C., Corfield, D. R., Tracey, I., et al. (2009b). Opioids depress cortical centers responsible for the volitional control of respiration. J. Neurosci. 29, 8177-8186. doi:10.1523/JNEUROSCI.1375-09. 2009
38. Pfeuffer, J., Van de Moortele, P.-F., Ugurbil, K., Hu, X., and Glover, G. H. (2002). Correction of physiologically induced global off-resonance effects in dynamic echo-planar and spiral functional imaging. Magn. Reson. Med. 47, 344-353. doi:10.1002/mrm.10065
39. Piché, M., Cohen-Adad, J., Nejad, M. K., Perlbarg, V., Xie, G., Beaudoin, G., et al. (2009). Characterization of cardiac-related noise in fMRI of the cervical spinal cord. Magn. Reson. Imaging 27, 300-310. doi: 10.1016/j. mri.2008.07.019
40. Poser, B. A., and Norris, D. G. (2009). Investigating the benefits of multi-echo EPI for fMRI at 7 T. Neuroimage 45, 1162-1172. doi:10. 1016/j.neuroimage.2009.01.007
41. Poser, B. A., Versluis, M. J., Hoogduin, J. M., and Norris, D. G. (2006). BOLD contrast sensitivity enhancement and artifact reduction with multiecho EPI: parallel-acquired inhomogeneity-desensitized fMRI. Magn. Reson. Med. 55, 1227-1235. doi:10.1002/mrm.20900
42. Purdon, P., and Weisskoff, R. (1998). Effect of temporal autocorrelation due to physiological noise and stimulus paradigm on voxel- level false-positive rates in fMRI. Hum. Brain Mapp. 6, 239-249. doi:10.1002/(SICI)1097- 0193(1998)6:4<239::AID-HBM4>3.0.CO;2-4
43. Raj, D., Anderson, A. W., and Gore, J. C. (2001). Respiratory effects in human functional magnetic resonance imaging due to bulk susceptibility changes. Phys. Med. Biol. 46, 3331-3340. doi:10.1088/0031-9155/46/12/318
44. Restom, K., Behzadi, Y., and Liu, T. T. (2006). Physiological noise reduction for arterial spin labeling functional MRI. Neuroimage 31, 1104-1115. doi:10.1016/j. neuroimage.2006.01.026
45. Setsompop, K., Gagoski, B. A., Poli- meni, J. R., Witzel, T., Wedeen, V. J., and Wald, L. L. (2012). Blipped- controlled aliasing in parallel imaging for simultaneous multislice echo planar imaging with reduced g- factor penalty. Magn. Reson. Med. 67, 1210-1224. doi:10.1002/mrm. 23097
46. Shmueli, K., van Gelderen, P., de Zwart, J. A., Horovitz, S. G., Fuku- naga, M., Jansma, J. M., et al. (2007). Low-frequency fluctuations in the cardiac rate as a source of variance in the resting-state fMRI BOLD signal. Neuroimage 38, 306-320. doi:10.1016/j.neuroimage. 2007.07.037
47. Smith, S. M., Beckmann, C. F., Andersson, J., Auerbach, E. J., Bijsterbosch, J., Douaud, G., et al. (2013a). Resting-state fMRI in the Human Connectome Project. Neuroimage 80, 144-168. doi:10.1016/j. neuroimage.2013.05.039
48. Smith, J. C., Abdala, A. P. L., Borgmann, A., Rybak, I. A., and Paton, J. F. R. (2013b). Brainstem respiratory networks: building blocks and microcircuits. Trends Neurosci. 36, 152-162. doi:10.1016/j.tins.2012.11. 004
49. Thomas, C. G., Harshman, R. A., and Menon, R. S. (2002). Noise reduction in BOLD-based fMRI using component analysis. Neuroimage 17, 1521-1537. doi:10.1006/nimg.2002. 1200
50. Tijssen, R. H., Jenkinson, M., Brooks, J. C., Jezzard, P., and Miller, K. L. (in press). Optimizing RetroICor and RetroKCor corrections for multi-shot 3D FMRI acquisitions. Neuroimage. doi:10. 1016/j.neuroimage.2013.08.062
51. Tohka, J., Foerde, K., Aron, A. R., Tom, S. M., Toga, A. W., and Poldrack, R. A. (2008). Automatic independent component labeling for artifact removal in fMRI. Neuroimage 39, 1227. doi:10.1016/j.neuroimage. 2007.10.013
52. Tousignant-Laflamme, Y., Rainville, P., and Marchand, S. (2005). Establishing a link between heart rate and pain in healthy subjects: a gender effect. J. Pain 6, 341-347. doi:10. 1016/j.jpain.2005.01.351
53. Triantafyllou, C., Hoge, R. D., Krueger, G, Wiggins, C. J., Potthast, A., Wiggins, G. C., et al. (2005). Comparison of physiological noise at 1.5 T, 3 T and 7 T and optimization of fMRI acquisition parameters. Neuroimage 26, 243-250. doi:10.1016/j.neuroimage.2005.01. 007
54. Windischberger, C., Langenberger, H., Sycha, T., Tschernko, E. M., Fuchsjäger-Mayerl, G., Schmetterer, L., et al. (2002). On the origin of respiratory artifacts in BOLD-EPI of the human brain. Magn. Reson. Imaging 20, 575-582. doi:10.1016/ S0730-725X(02)00563-5
55. Wise, R. G., Ide, K., Poulin, M. J., and Tracey, I. (2004). Resting fluctuations in arterial carbon dioxide induce significant low frequency variations in BOLD signal. Neuroimage 21, 1652-1664. doi:10.1016/j.neuroimage.2003.11.025
56. Wise, R. G., Pattinson, K. T. S., Bulte, D. P., Chiarelli, P. A., Mayhew, S. D., Balanos, G. M., et al. (2007). Dynamic forcing of end-tidal carbon dioxide and oxygen applied to functional magnetic resonance imaging. J. Cereb. BloodFlowMetab. 27, 1521-1532. doi:10.1038/sj.jcbfm. 9600465
57. Woolrich, M. W., Ripley, B. D., Brady, M., and Smith, S. M. (2001). Temporal autocorrelation in univariate linear modelling ofFMRI data. Neuroimage 14,1370-1386. doi:10.1006/nimg.2001.0931
58. Xie, G., Piche, M., Khoshnejad, M., Perlbarg, V., Chen, J.-I., Hoge, R. D., et al. (2012). Reduction of physiological noise with independent component analysis improves the detection of nociceptive responses with fMRI of the human spinal cord. Neuroimage 63, 245-252. doi:10.1016/j.neuroimage. 2012.06.057
59. Zhang, W.-T., Mainero, C., Kumar, A., Wiggins, C. J., Benner, T., Purdon, P. L., et al. (2006). Strategies for improving the detection of fMRI activation in trigeminal pathways with cardiac gating. Neuroimage 31, 1506-1512. doi:10.1016/j.neuroimage.2006.02.033