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Clinical Neuroradiology
Published in: Clinical Neuroradiology 2/2015

01-10-2015 | Review Article

Functional MRI of the Brainstem: Common Problems and their Solutions

Author: F. Beissner

Published in: Clinical Neuroradiology | Special Issue 2/2015

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Abstract

Functional magnetic resonance imaging (fMRI) of the brainstem is a relatively young field that is rapidly evolving. While it is still difficult to obtain usable fMRI signals from this complicated brain region, the past few years have seen a number of important advances that bring us closer to routine application of this method in the clinical and scientific setting. This review gives an overview of the technical capabilities and limitations of brainstem fMRI. It explains the major brainstem-specific problems and gives advice on how to avoid or counteract them. In particular, I discuss how spatial resolution issues can be overcome by using appropriate sequences, coils, and spatial preprocessing, how the effects of physiological noise can be mitigated by noise modeling and spatial masking, and how the functional heterogeneity of brainstem nuclei needs to be taken into account, when planning a study. Solving these common problems is a prerequisite for any scientist or clinician interested in applying fMRI to measure brainstem activity.
Footnotes
1
For the state of the art in structural brainstem MRI the reader is referred to Beissner and Baudrexel [36].
 
Literature
1.
Jänig W. Integrative action of the autonomic nervous system: neurobiology of homeostasis. Cambridge: Cambridge University Press; 2008.
2.
Naidich TP, Duvernoy HM, Delman BN, Sorensen AG, Kollias SS, Haacke EM. Duvernoy’s atlas of the human brain stem and cerebellum: high-field MRI, surface anatomy, internal structure, vascularization and 3 D sectional anatomy. Wien: Springer; 2008.
3.
Paxinos GT, Huang XF. Atlas of the human brainstem. Waltham, MA: Academic Press; 1995.
4.
Heinricher MM, Tavares I, Leith JL, Lumb BM. Descending control of nociception: specificity, recruitment and plasticity. Brain Res Rev. 2009;60:214–25.PubMedCentralCrossRefPubMed
5.
Afshar F, Watkins ES, Yap JC. Stereotaxic atlas of the human brainstem and cerebellar nuclei. A variability study. New York: Raven Press; 1978.
6.
Haacke EM, Brown R, Thompson M, Venkatesan R. Magnetic resonance imaging: physical principles and sequence design. New York: Wiley-Liss; 1999.
7.
Worsley KJ, Friston KJ. Analysis of fMRI time-series revisited—again. Neuroimage. 1995;2:173–81.CrossRefPubMed
8.
Beissner F, Deichmann R, Baudrexel S. fMRI of the brainstem using dual-echo EPI. Neuroimage. 2011;55:1593–9.CrossRefPubMed
9.
Cohen-Adad J, Mareyam A, Keil B, Polimeni JR, Wald LL. 32-Channel RF coil optimized for brain and cervical spinal cord at 3 T. Magn Reson Med. 2011;66:1198–208.PubMedCentralCrossRefPubMed
10.
Parrish TB, Gitelman DR, LaBar KS, Mesulam MM. Impact of signal-to-noise on functional MRI. Magn Reson Med. 2000;44:925–32.CrossRefPubMed
11.
Napadow V, Dhond R, Park K, Kim J, Makris N, Kwong KK, Harris RE, Purdon PL, Kettner N, Hui KK. Time-variant fMRI activity in the brainstem and higher structures in response to acupuncture. Neuroimage. 2009;47:289–301.PubMedCentralCrossRefPubMed
12.
Pattinson KTS, Mitsis GD, Harvey AK, Jbabdi S, Dirckx S, Mayhew SD, Rogers R, Tracey I, Wise RG. Determination of the human brainstem respiratory control network and its cortical connections in vivo using functional and structural imaging. Neuroimage. 2009;44:295–305.CrossRefPubMed
13.
Hutton C, Bork A, Josephs O, Deichmann R, Ashburner J, Turner R. Image distortion correction in fMRI: a quantitative evaluation. Neuroimage. 2002;16:217–40.CrossRefPubMed
14.
Diedrichsen J. A spatially unbiased atlas template of the human cerebellum. Neuroimage. 2006;33:127–38.CrossRefPubMed
15.
Napadow V, Dhond R, Kennedy D, Hui KKS, Makris N. Automated brainstem co-registration (ABC) for MRI. Neuroimage. 2006;32:1113–9.CrossRefPubMed
16.
17.
Andersson JLR, Jenkinson M, Smith SM. Non-linear registration aka Spatial normalisation FMRIB Technial Report TR07JA2. 2007.
18.
Jenkinson M, Smith SM. A global optimisation method for robust affine registration of brain images. Med Image Anal. 2001;5:143–56.CrossRefPubMed
19.
Jezzard P. Physiological noise: strategies for correction. In: Moonen C, Bandettini PA, editors. Functional MRI. Berlin: Springer-Verlag; 1999. pp. 171–9.
20.
Raj D, Anderson a W, Gore JC. Respiratory effects in human functional magnetic resonance imaging due to bulk susceptibility changes. Phys Med Biol. 2001;46:3331–40.CrossRefPubMed
21.
Dagli MS, Ingeholm JE, Haxby JV. Localization of cardiac-induced signal change in fMRI. Neuroimage. 1999;9:407–15.CrossRefPubMed
22.
Greitz D, Wirestam R, Franck A, Nordell B, Thomsen C. Pulsatile brain movement and associated hydrodynamics studied by magnetic resonance phase imaging. Neuroradiology. 1992;34:370–80.CrossRefPubMed
23.
Glover G, Li TQ, Ress D. Image-based method for retrospective correction of physiological motion effects in fMRI: RETROICOR. Magn Reson Med. 2000;44:162–7.CrossRefPubMed
24.
25.
Guimaraes AR, Melcher JR, Talavage TM, Baker JR, Ledden P, Rosen BR, Kiang NY, Fullerton BC, Weisskoff RM. Imaging subcortical auditory activity in humans. Hum Brain Mapp. 1998;6:33–41.PubMedCentralCrossRefPubMed
26.
Beissner F, Baudrexel S, Volz S, Deichmann R. Dual-echo EPI for non-equilibrium fMRI—Implications of different echo combinations and masking procedures. Neuroimage. 2010;52:524–31.CrossRefPubMed
27.
Beissner F, Schumann A, Brunn F, Eisenträger D, Bär K. Advances in functional magnetic resonance imaging of the human brainstem. Neuroimage. 2014;86:91–8.CrossRefPubMed
28.
Beckmann CF, DeLuca M, Devlin JT, Smith SM. Investigations into resting-state connectivity using independent component analysis. Philos Trans R Soc Lond B Biol Sci. 2005;360:1001–13.PubMedCentralCrossRefPubMed
29.
Kong Y, Eippert F, Beckmann CF, Andersson J, Finsterbusch J, Büchel C, Tracey I, Brooks JC. Intrinsically organized resting state networks in the human spinal cord. Proc Natl Acad Sci U S A. 2014;111:18067–72.PubMedCentralCrossRefPubMed
30.
Lambert C, Chowdhury R, FitzGerald T, Fleming S, Lutti A, Hutton C, Draganski B, Frackowiak R, Ashburner J. Characterizing aging in the human brainstem using quantitative multimodal MRI analysis. Front Hum Neurosci. 2013;7:462.PubMedCentralCrossRefPubMed
31.
Pattinson KTS, Governo RJ, MacIntosh BJ, Russell EC, Corfield DR, Tracey I, Wise RG. Opioids depress cortical centers responsible for the volitional control of respiration. J Neurosci. 2009;29:8177–86.CrossRefPubMed
32.
De Luca M, Beckmann CF, De Stefano N, Matthews PM, Smith SM. fMRI resting state networks define distinct modes of long-distance interactions in the human brain. Neuroimage. 2006;29:1359–67.CrossRefPubMed
33.
Eippert F, Bingel U, Schoell ED, Yacubian J, Klinger R, Lorenz J, Büchel C. Activation of the opioidergic descending pain control system underlies placebo analgesia. Neuron. 2009;63:533–43.CrossRefPubMed
34.
Baudrexel S, Witte T, Seifried C, von Wegner F, Beissner F, Klein JC, Steinmetz H, Deichmann R, Roeper J, Hilker R. Resting state fMRI reveals increased subthalamic nucleus-motor cortex connectivity in Parkinson’s disease. Neuroimage. Elsevier Inc.; 2011;55:1728–38.CrossRefPubMed
35.
Macefield VG, Henderson LA. Real-time imaging of the medullary circuitry involved in the generation of spontaneous muscle sympathetic nerve activity in awake subjects. Hum Brain Mapp. 2010;31:539–49.PubMed
36.
Beissner F, Baudrexel S, editors. Investigating the human brainstem with structural and functional MRI. Frontiers of Human Neuroscience; 2014.
Metadata
Title
Functional MRI of the Brainstem: Common Problems and their Solutions
Author
F. Beissner
Publication date
01-10-2015
Publisher
Springer Berlin Heidelberg
Published in
Clinical Neuroradiology / Issue Special Issue 2/2015
Print ISSN: 1869-1439
Electronic ISSN: 1869-1447
DOI
https://doi.org/10.1007/s00062-015-0404-0

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