Identification and characterisation of midbrain nuclei using optimised functional magnetic resonance imaging

Limbrick-Oldfield, Eve H., Brooks, Jonathan C.W. ORCID: https://orcid.org/0000-0003-3335-6209, Wise, Richard J.S., Padormo, Francesco, Hajnal, Jo V., Beckmann, Christian F. and Ungless, Mark A. (2012) Identification and characterisation of midbrain nuclei using optimised functional magnetic resonance imaging. NeuroImage, 59 (2). pp. 1230-1238. ISSN 1053-8119

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Abstract

Localising activity in the human midbrain with conventional functional MRI (fMRI) is challenging because the midbrain nuclei are small and located in an area that is prone to physiological artefacts. Here we present a replicable and automated method to improve the detection and localisation of midbrain fMRI signals. We designed a visual fMRI task that was predicted would activate the superior colliculi (SC) bilaterally. A limited number of coronal slices were scanned, orientated along the long axis of the brainstem, whilst simultaneously recording cardiac and respiratory traces. A novel anatomical registration pathway was used to optimise the localisation of the small midbrain nuclei in stereotactic space. Two additional structural scans were used to improve registration between functional and structural T1-weighted images: an echo-planar image (EPI) that matched the functional data but had whole-brain coverage, and a whole-brain T2-weighted image. This pathway was compared to conventional registration pathways, and was shown to significantly improve midbrain registration. To reduce the physiological artefacts in the functional data, we estimated and removed structured noise using a modified version of a previously described physiological noise model (PNM). Whereas a conventional analysis revealed only unilateral SC activity, the PNM analysis revealed the predicted bilateral activity. We demonstrate that these methods improve the measurement of a biologically plausible fMRI signal. Moreover they could be used to investigate the function of other midbrain nuclei.

Item Type: Article
Additional Information: Funding Information: We thank the volunteers for taking part in this study, and Emer Hughes and Amy McGuinness for assistance with the data collection. This work was supported by grant U120085816 from the U.K. Medical Research Council (MRC) and a University Research Fellowship from The Royal Society to M.A.U., by grant U120064975 from the U.K. MRC to R.J.S.W., and a Career Development Award from the U.K. MRC to J.C.W.B.
Uncontrolled Keywords: fmri,midbrain,physiological noise,registration,superior colliculi,neurology,cognitive neuroscience ,/dk/atira/pure/subjectarea/asjc/2800/2808
Faculty \ School: Faculty of Social Sciences > School of Psychology
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Depositing User: LivePure Connector
Date Deposited: 07 Sep 2022 11:32
Last Modified: 22 Sep 2022 18:32
URI: https://ueaeprints.uea.ac.uk/id/eprint/87809
DOI: 10.1016/j.neuroimage.2011.08.016

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