Towards HCP-Style macaque connectomes: 24-Channel 3T multi-array coil, MRI sequences and preprocessing

Autio, Joonas; Glasser, Matthew F.; Ose, Takayuki; Donahue, Chad J.; Bastiani, Matteo; Ohno, Masahiro; Kawabata, Yoshihiko; Urushibata, Yuta; Murata, Katsutoshi; Nishigori, Kantaro; Yamaguchi, Masataka; Hori, Yuki; Yoshida, Atsushi; Go, Yasuhiro; Coalson, Timothy S.; Jbabdi, Saâd; Sotiropoulos, Stamatios N.; Kennedy, Henry; Smith, Stephen M.; Essen, David C. Van; Hayashi, Takuya

doi:10.1016/j.neuroimage.2020.116800

Cited by 78 publications

(134 citation statements)

References 80 publications

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“…12 is qualitatively similar to that of published maps of individual subjects (see Koo et al 2012;Oguz et al 2015; Fig. 4 of Autio et al 2020) and group averages (see Fig. 3 of Koo et al 2012, n=8; Fig.…”

Section: Discussionsupporting

confidence: 87%

“…The average cortical thickness map across the 29 subjects and its coefficient of variation (COV=standard deviation/mean) are shown in Figure 12 . The cortical thickness map patterns follow closely those obtained from human MRIs processed with CIVET, with cortical thickness increasing from posterior to anterior, as well as published macaque cortical thickness maps (Autio et al 2020;Calebrese et al 2015;Donahue et al 2018;Koo et al 2012). The COV was low in most regions.…”

Section: Cortical Thicknesssupporting

confidence: 77%

“…These values are larger than those reported for the macaque (Autio et al 2020;Donahue et al 2018;Koo et al 2012), even when accounting for the mid-plane wall region. The larger values obtained here could be an indication of deeper sulcal penetration of the pial surface and increased morphological details captured by the extracted surfaces.…”

Section: Surface Areacontrasting

confidence: 73%

“…Cortical thickness values for the insula are likely slightly inflated in t hese cases. The WM surface in this region was, however, smooth and did not exhibit the 'claustrum invagination problem' (Autio et al 2020). Nor were there issues with segmentation in such problem areas as the ventral and anterior claustrum or the temporal stem.…”

Section: Cortical Surface Generationmentioning

confidence: 79%

“…Several cortical surface reconstructions for macaques have been presented (Koo et al 2012;Oguz et al 2015;Donahue et al 2018;Wang et al 2018;Autio et al 2020) and a few new pipelines for macaque cortical surface generation have recently been shared on the PRIME-Resource Exchange ( https://prime-re.github.io/ ) (Messinger et al, this issue ). These efforts have made surface generation less labor intensive .…”

Section: Introductionmentioning

confidence: 99%

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CIVET-Macaque: an automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques

Lepage

Wagstyl

Jung

et al. 2020

Preprint

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The MNI CIVET pipeline for automated extraction of cortical surfaces and evaluation of cortical thickness from in-vivo human MRI has been extended for processing macaque brains. Processing is performed based on the NIMH Macaque Template (NMT), as the reference template, with the anatomical parcellation of the surface following the D99 and CHARM atlases. The modifications needed to adapt CIVET to the macaque brain are detailed. Results have been obtained using CIVET-macaque to process the anatomical scans of the 31 macaques used to generate the NMT and another 95 macaques from the PRIME-DE initiative. It is anticipated that the open usage of CIVET-macaque will promote collaborative efforts in data collection and processing, sharing, and automated analyses from which the non-human primate brain imaging field will advance.

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Section: Discussionsupporting

confidence: 87%

Section: Cortical Thicknesssupporting

confidence: 77%

Section: Surface Areacontrasting

confidence: 73%

Section: Cortical Surface Generationmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

CIVET-Macaque: an automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques

Lepage

Wagstyl

Jung

et al. 2020

Preprint

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Model‐based dynamic off‐resonance correction for improved accelerated fMRI in awake behaving nonhuman primates

Shahdloo

Schüffelgen

Papp

et al. 2022

Magnetic Resonance in Med

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To estimate dynamic off-resonance due to vigorous body motion in accelerated fMRI of awake behaving nonhuman primates (NHPs) using the echo-planar imaging reference navigator, in order to attenuate the effects of timevarying off-resonance on the reconstruction. Methods:In NHP fMRI, the animal's head is usually head-posted, and the dynamic off-resonance is mainly caused by motion in body parts that are distant from the brain and have low spatial frequency. Hence, off-resonance at each frame can be approximated as a spatially linear perturbation of the off-resonance at a reference frame, and is manifested as a relative linear shift in k-space. Using GRAPPA operators, we estimated these shifts by comparing the navigator at each time frame with that at the reference frame. Estimated shifts were then used to correct the data at each frame. The proposed method was evaluated in phantom scans, simulations, and in vivo data. Results:The proposed method is shown to successfully estimate spatially low-order dynamic off-resonance perturbations, including induced linear offresonance perturbations in phantoms, and is able to correct retrospectively corrupted data in simulations. Finally, it is shown to reduce ghosting artifacts and geometric distortions by up to 20% in simultaneous multislice in vivo acquisitions in awake-behaving NHPs. Conclusion:A method is proposed that does not need sequence modification or extra acquisitions and makes accelerated awake behaving NHP imaging more robust and reliable, reducing the gap between what is possible with NHP protocols and state-of-the-art human imaging.

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Cortical adaptation of the night monkey to a nocturnal niche environment: a comparative non-invasive T1w/T2w myelin study

et al. 2022

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Night monkeys (Aotus) are the only genus of monkeys within the Simian lineage that successfully occupy a nocturnal environmental niche. Their behavior is supported by their sensory organs’ distinctive morphological features; however, little is known about their evolutionary adaptations in sensory regions of the cerebral cortex. Here, we investigate this question by exploring the cortical organization of night monkeys using high-resolution in-vivo brain MRI and comparative cortical-surface T1w/T2w myeloarchitectonic mapping. Our results show that the night monkey cerebral cortex has a qualitatively similar but quantitatively different pattern of cortical myelin compared to the diurnal macaque and marmoset monkeys. T1w/T2w myelin and its gradient allowed us to parcellate high myelin areas, including the middle temporal complex (MT +) and auditory cortex, and a low-myelin area, Brodmann area 7 (BA7) in the three species, despite species differences in cortical convolutions. Relative to the total cortical-surface area, those of MT + and the auditory cortex are significantly larger in night monkeys than diurnal monkeys, whereas area BA7 occupies a similar fraction of the cortical sheet in all three species. We propose that the selective expansion of sensory areas dedicated to visual motion and auditory processing in night monkeys may reflect cortical adaptations to a nocturnal environment.

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Towards HCP-Style macaque connectomes: 24-Channel 3T multi-array coil, MRI sequences and preprocessing

Cited by 78 publications

References 80 publications

CIVET-Macaque: an automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques

CIVET-Macaque: an automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques

Model‐based dynamic off‐resonance correction for improved accelerated fMRI in awake behaving nonhuman primates

Cortical adaptation of the night monkey to a nocturnal niche environment: a comparative non-invasive T1w/T2w myelin study

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