Towards HCP-Style macaque connectomes: 24-Channel 3T multi-array coil, MRI sequences and preprocessing
Joonas A. Autio,
Matthew F. Glasser,
Takayuki Ose,
Chad J. Donahue,
Matteo Bastiani,
Masahiro Ohno,
Yoshihiko Kawabata,
Yuta Urushibata,
Katsutoshi Murata,
Kantaro Nishigori,
Masataka Yamaguchi,
Yuki Hori,
Atsushi Yoshida,
Yasuhiro Go,
Timothy S. Coalson,
Saad Jbabdi,
Stamatios N. Sotiropoulos,
Henry Kennedy,
Stephen Smith,
David C. Van Essen,
Takuya Hayashi
Affiliations
Joonas A. Autio
Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
Matthew F. Glasser
Department of Neuroscience, Washington University School of Medicine, St Louis, Missouri, USA; Department of Radiology, Washington University School of Medicine, St Louis, MO, USA; St. Luke’s Hospital, St. Louis, Missouri, USA
Takayuki Ose
Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
Chad J. Donahue
Department of Neuroscience, Washington University School of Medicine, St Louis, Missouri, USA
Matteo Bastiani
Wellcome Centre for Integrative Neuroimaging, Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), University of Oxford, Oxford, United Kingdom; Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom; National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Queens Medical Centre, Nottingham, UK
Masahiro Ohno
Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
Yoshihiko Kawabata
Takashima Seisakusho Co., Ltd, Tokyo, Japan
Yuta Urushibata
Siemens Healthcare Japan, Tokyo, Japan
Katsutoshi Murata
Siemens Healthcare Japan, Tokyo, Japan
Kantaro Nishigori
Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Sumitomo Dainippon Pharma Co., Ltd, Osaka, Japan
Masataka Yamaguchi
Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Sumitomo Dainippon Pharma Co., Ltd, Osaka, Japan
Yuki Hori
Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
Atsushi Yoshida
Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
Yasuhiro Go
Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan; Department of System Neuroscience, National Institute for Physiological Sciences, Okazaki, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
Timothy S. Coalson
Department of Neuroscience, Washington University School of Medicine, St Louis, Missouri, USA
Saad Jbabdi
Wellcome Centre for Integrative Neuroimaging, Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), University of Oxford, Oxford, United Kingdom
Stamatios N. Sotiropoulos
Wellcome Centre for Integrative Neuroimaging, Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), University of Oxford, Oxford, United Kingdom; Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom; National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Queens Medical Centre, Nottingham, UK
Henry Kennedy
Université Lyon, Université Claude Bernard Lyon, France; Inserm, Stem Cell and Brain Research Institute, Bron, France; Institute of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
Stephen Smith
Wellcome Centre for Integrative Neuroimaging, Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB), University of Oxford, Oxford, United Kingdom
David C. Van Essen
Department of Neuroscience, Washington University School of Medicine, St Louis, Missouri, USA
Takuya Hayashi
Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Corresponding author. Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
Macaque monkeys are an important animal model where invasive investigations can lead to a better understanding of the cortical organization of primates including humans. However, the tools and methods for noninvasive image acquisition (e.g. MRI RF coils and pulse sequence protocols) and image data preprocessing have lagged behind those developed for humans. To resolve the structural and functional characteristics of the smaller macaque brain, high spatial, temporal, and angular resolutions combined with high signal-to-noise ratio are required to ensure good image quality. To address these challenges, we developed a macaque 24-channel receive coil for 3-T MRI with parallel imaging capabilities. This coil enables adaptation of the Human Connectome Project (HCP) image acquisition protocols to the in-vivo macaque brain. In addition, we adapted HCP preprocessing methods to the macaque brain, including spatial minimal preprocessing of structural, functional MRI (fMRI), and diffusion MRI (dMRI). The coil provides the necessary high signal-to-noise ratio and high efficiency in data acquisition, allowing four- and five-fold accelerations for dMRI and fMRI. Automated FreeSurfer segmentation of cortex, reconstruction of cortical surface, removal of artefacts and nuisance signals in fMRI, and distortion correction of dMRI all performed well, and the overall quality of basic neurobiological measures was comparable with those for the HCP. Analyses of functional connectivity in fMRI revealed high sensitivity as compared with those from publicly shared datasets. Tractography-based connectivity estimates correlated with tracer connectivity similarly to that achieved using ex-vivo dMRI. The resulting HCP-style in vivo macaque MRI data show considerable promise for analyzing cortical architecture and functional and structural connectivity using advanced methods that have previously only been available in studies of the human brain.
