title: ICA-based artefact removal and accelerated fMRI acquisition for improved resting state network imaging.
abstract: The identification of resting state networks (RSNs) and the quantification of their functional connectivity in resting-state fMRI (rfMRI) are seriously hindered by the presence of artefacts, many of which overlap spatially or spectrally with RSNs. Moreover, recent developments in fMRI acquisition yield data with higher spatial and temporal resolutions, but may increase artefacts both spatially and/or temporally. Hence the correct identification and removal of non-neural fluctuations is crucial, especially in accelerated acquisitions. In this paper we investigate the effectiveness of three data-driven cleaning procedures, compare standard against higher (spatial and temporal) resolution accelerated fMRI acquisitions, and investigate the combined effect of different acquisitions and different cleanup approaches. We applied single-subject independent component analysis (ICA), followed by automatic component classification with FMRIB's ICA-based X-noiseifier (FIX) to identify artefactual components. We then compared two first-level (within-subject) cleaning approaches for removing those artefacts and motion-related fluctuations from the data. The effectiveness of the cleaning procedures was assessed using time series (amplitude and spectra), network matrix and spatial map analyses. For time series and network analyses we also tested the effect of a second-level cleaning (informed by group-level analysis). Comparing these approaches, the preferable balance between noise removal and signal loss was achieved by regressing out of the data the full space of motion-related fluctuations and only the unique variance of the artefactual ICA components. Using similar analyses, we also investigated the effects of different cleaning approaches on data from different acquisition sequences. With the optimal cleaning procedures, functional connectivity results from accelerated data were statistically comparable or significantly better than the standard (unaccelerated) acquisition, and, crucially, with higher spatial and temporal resolution. Moreover, we were able to perform higher dimensionality ICA decompositions with the accelerated data, which is very valuable for detailed network analyses.
authors.affiliation: FMRIB (Oxford University Centre for Functional MRI of the Brain), UK; Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy; MR Laboratory, IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy. Electronic address: lgriffanti@dongnocchi.it.
authors.forename: Ludovica
authors.initials: L
authors.lastname: Griffanti
authors.affiliation: FMRIB (Oxford University Centre for Functional MRI of the Brain), UK.
authors.forename: Gholamreza
authors.initials: G
authors.lastname: Salimi-Khorshidi
authors.affiliation: Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands; MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands.
authors.forename: Christian F
authors.initials: CF
authors.lastname: Beckmann
authors.affiliation: Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: Auerbach
authors.affiliation: FMRIB (Oxford University Centre for Functional MRI of the Brain), UK.
authors.forename: Gwenaëlle
authors.initials: G
authors.lastname: Douaud
authors.affiliation: Department of Psychiatry, University of Oxford, Oxford, UK.
authors.forename: Claire E
authors.initials: CE
authors.lastname: Sexton
authors.affiliation: Department of Psychiatry, University of Oxford, Oxford, UK.
authors.forename: Enikő
authors.initials: E
authors.lastname: Zsoldos
authors.affiliation: Department of Psychiatry, University of Oxford, Oxford, UK.
authors.forename: Klaus P
authors.initials: KP
authors.lastname: Ebmeier
authors.affiliation: FMRIB (Oxford University Centre for Functional MRI of the Brain), UK; Department of Psychiatry, University of Oxford, Oxford, UK.
authors.forename: Nicola
authors.initials: N
authors.lastname: Filippini
authors.affiliation: FMRIB (Oxford University Centre for Functional MRI of the Brain), UK; Department of Psychiatry, University of Oxford, Oxford, UK.
authors.forename: Clare E
authors.initials: CE
authors.lastname: Mackay
authors.affiliation: Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA.
authors.forename: Steen
authors.initials: S
authors.lastname: Moeller
authors.affiliation: Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA; Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
authors.forename: Junqian
authors.initials: J
authors.lastname: Xu
authors.affiliation: Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA.
authors.forename: Essa
authors.initials: E
authors.lastname: Yacoub
authors.affiliation: Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Baselli
authors.affiliation: Center for Magnetic Resonance Research, University of Minnesota Medical School, Minneapolis, MN, USA.
authors.forename: Kamil
authors.initials: K
authors.lastname: Ugurbil
authors.affiliation: FMRIB (Oxford University Centre for Functional MRI of the Brain), UK.
authors.forename: Karla L
authors.initials: KL
authors.lastname: Miller
authors.affiliation: FMRIB (Oxford University Centre for Functional MRI of the Brain), UK.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Smith
mesh_terms: D000368:Aged; D000465:Algorithms; D016477:Artifacts; D001921:Brain / Q000502:physiology*; D001931:Brain Mapping / Q000379:methods*; D005260:Female; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D008875:Middle Aged; D009434:Neural Pathways / Q000502:physiology; D012146:Rest
keywords: Artefact removal; Functional connectivity; Functional magnetic resonance imaging (fMRI); Multiband acceleration; Resting-state