RT Journal Article
SR Electronic
T1 Towards HCP-Style Macaque Connectomes: 24-Channel 3T Multi-Array Coil, MRI Sequences and Preprocessing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 602979
DO 10.1101/602979
A1 Joonas A. Autio
A1 Matthew F. Glasser
A1 Takayuki Ose
A1 Chad J. Donahue
A1 Matteo Bastiani
A1 Masahiro Ohno
A1 Yoshihiko Kawabata
A1 Yuta Urushibata
A1 Katsutoshi Murata
A1 Kantaro Nishigori
A1 Masataka Yamaguchi
A1 Yuki Hori
A1 Atsushi Yoshida
A1 Yasuhiro Go
A1 Timothy S. Coalson
A1 Saad Jbabdi
A1 Stamatios N. Sotiropoulos
A1 Stephen Smith
A1 David C. Van Essen
A1 Takuya Hayashi
YR 2019
UL http://biorxiv.org/content/early/2019/04/09/602979.abstract
AB Macaque monkeys are an important model species for understanding cortical organization of primates, yet 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 relatively thin macaque cortex, high spatial, temporal, and angular resolutions are required while maintaining high signal-to-noise ratio 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 enabled adaptation of the Human Connectome Project (HCP) image acquisition protocols to the macaque brain. We also adapted HCP preprocessing methods optimized for the macaque brain, including spatial minimal preprocessing of structural, functional MRI (fMRI), and diffusion MRI (dMRI). The coil provided high signal-to-noise ratio and high efficiency in data acquisition, allowing four- and five-fold acceleration for dMRI and fMRI, respectively. Automated parcellation of cortex, reconstruction of cortical surface, removal of artefacts and nuisance signals in fMRI, and distortion correction of dMRI performed well, and the overall quality of basic neurobiological measures was comparable with those for the HCP. 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 for humans.Highlights➢ 24-channel 3T MR receive coil designed for the smaller macaque brain.➢ In vivo macaque imaging protocols adapted according to guidelines from the HCP.➢ Parallel imaging yields five- and four-fold acceleration in fMRI and dMRI sampling.➢ HCP’s minimal preprocessing and denoising pipelines adapted for macaques.➢ The multi-modal MRI data show considerable promise for HCP-style analyses.