Towards HCP-Style Macaque Connectomes: 24-Channel 3T Multi-Array Coil, MRI Sequences and Preprocessing

Autio, J. A.; Glasser, M. F.; Ose, T.; Donahue, C. J.; Bastiani, M.; Ohno, M.; Kawabata, Y.; Urushibata, Y.; Murata, K.; Nishigori, K.; Yamaguchi, M.; Hori, Y.; Yoshida, A.; Go, Y.; Coalson, T. S.; Jbabdi, S.; Sotiropoulos, S. N.; Smith, S.; Van Essen, D. C.; Hayashi, T.

doi:10.1101/602979

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bioRxiv · 10.1101/602979

Towards HCP-Style Macaque Connectomes: 24-Channel 3T Multi-Array Coil, MRI Sequences and Preprocessing

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Abstract

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.\n\nHighlights[tpltrtarr] 24-channel 3T MR receive coil designed for the smaller macaque brain.\n[tpltrtarr]In vivo macaque imaging protocols adapted according to guidelines from the HCP.\n[tpltrtarr]Parallel imaging yields five- and four-fold acceleration in fMRI and dMRI sampling.\n[tpltrtarr]HCPs minimal preprocessing and denoising pipelines adapted for macaques.\n[tpltrtarr]The multi-modal MRI data show considerable promise for HCP-style analyses.

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Autio, J. A., Glasser, M. F., Ose, T., Donahue, C. J., Bastiani, M., Ohno, M., Kawabata, Y., Urushibata, Y., Murata, K., Nishigori, K., Yamaguchi, M., Hori, Y., Yoshida, A., Go, Y., Coalson, T. S., Jbabdi, S., Sotiropoulos, S. N., Smith, S., Van Essen, D. C., Hayashi, T.. 2019-04-09. Towards HCP-Style Macaque Connectomes: 24-Channel 3T Multi-Array Coil, MRI Sequences and Preprocessing. https://doi.org/10.1101/602979

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