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.; Smith, Stephen M.; Essen, David C. Van; Hayashi, Takuya

doi:10.1101/602979

Cited by 3 publications

(2 citation statements)

References 72 publications

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“…The respective results demonstrate the generalisability of our method to the macaque brain. Recent efforts to obtain macaque data from larger cohorts (HCP-style protocols) are ongoing (Autio et al, 2019;Milham et al, 2018) and our tools will be a useful resource for these new initiatives for the non-human primate brain (Thiebaut de Schotten et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

XTRACT - Standardised protocols for automated tractography in the human and macaque brain

Warrington

Bryant

et al. 2019

Preprint

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We present a new toolbox and library of standardised tractography protocols devised for the robust automated extraction of white matter tracts both in the human and the macaque brain. Using in vivo data from the Human Connectome Project (HCP) and the UK Biobank and ex vivo data for the macaque brain datasets, we obtain white matter atlases, as well as atlases for tract endpoints on the white-grey matter boundary, for both species. We illustrate that our protocols are robust against data quality, generalisable across two species and reflect the known anatomy. We further demonstrate that they capture inter-subject variability by preserving tract lateralisation in humans and tract similarities stemming from twinship in the HCP cohort. Our results demonstrate that the presented toolbox will be useful for generating imaging-derived features in large cohorts, and in facilitating comparative neuroanatomy studies. The software, tractography protocols, and atlases are publicly released through FSL, allowing users to define their own tractography protocols in a standardised manner, further contributing to open science.

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Section: Discussionmentioning

confidence: 99%

XTRACT - Standardised protocols for automated tractography in the human and macaque brain

Warrington

Bryant

et al. 2019

Preprint

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“…Additionally, they are a prerequisite for generating cortical flat maps, which are useful tools for the analysis and visualization of functional and structural neuroimaging datasets (Sultan et al, 2010;Van Essen et al, 1998;Vanduffel et al, 2001;Vanduffel et al, 2014), particularly for topographic representations such as retinotopy (Arcaro and Livingstone, 2017;Janssens et al, 2014), somatotopy (Arcaro et al, 2019) and tonotopy (Bodin et al, 2021;Erb et al, 2019;Petkov et al, 2006). To achieve this, a human-curated white and gray matter segmentation was performed with FreeSurfer (Fischl, 2012) (Autio et al, 2020), using a combination of T1 and T2 images (Autio et al, 2021). The pial and white/gray matter interface (white matter surface) was generated from the T1 images to create the MEBRAINS surface template.…”

Section: Generation Of a Mebrains Surface Templatementioning

confidence: 99%

MEBRAINS 1.0: a new population-based macaque atlas

Balan,

Zhu,

et al. 2023

Preprint

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Due to their fundamental relevance, the number of anatomical macaque brain templates is constantly growing. Novel templates aim to alleviate limitations of previously published atlases and offer the foundation to integrate multiscale multimodal data. Typical limitations of existing templates include their reliance on one subject, their unimodality (usually only T1 or histological images), or lack of anatomical details. The MEBRAINS template overcomes these limitations by using a combination of T1 and T2 images, from the same 10 animals (Macaca mulatta), which are averaged by the multi-brain toolbox for diffeomorphic registration and segmentation. The resulting volumetric T1 and T2 templates are supplemented with high quality white and gray matter surfaces built with FreeSurfer. Human-curated segmentations of pial surface, white/gray matter interface and major subcortical nuclei were used to analyse the relative quality of the MEBRAINS template. Recently published 3D maps of the macaque inferior parietal lobe and (pre)motor cortex were warped to the MEBRAINS surface template, thus populating it with a parcellation scheme based on cyto- and receptor architectonic analyses. Finally, 9 CT scans of the same monkeys were registered to the T1 modality and co-registered to the template. Through its main features (multi-subject, multi-modal, volume-and-surface, traditional and deep learning-based segmentations), MEBRAINS aims to improve integration of multi-modal multi-scale macaque data and is quantitatively equal or better compared to currently widely used macaque templates. The template is integrated in the EBRAINS and Scalable Brain Atlas web-based infrastructures, each of which comes with its own suite of spatial registration tools.

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Cross-species functional alignment reveals evolutionary hierarchy within the connectome

et al. 2020

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Evolution provides an important window into how cortical organization shapes function and vice versa. The complex mosaic of changes in brain morphology and functional organization that have shaped the mammalian cortex during evolution, complicates attempts to chart cortical differences across species. It limits our ability to fully appreciate how evolution has shaped our brain, especially in systems associated with unique human cognitive capabilities that lack anatomical homologues in other species. Here, we develop a function-based method for cross-species alignment that enables the quantification of homologous regions between humans and rhesus macaques, even when their location is decoupled from anatomical landmarks. Critically, we find cross-species similarity in functional organization reflects a gradient of evolutionary change that decreases from unimodal systems and culminates with the most pronounced changes in posterior regions of the default mode network (angular gyrus, posterior cingulate and middle temporal cortices). Our findings suggest that the establishment of the default mode network, as the apex of a cognitive hierarchy, has changed in a complex manner during human evolution – even within subnetworks.

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

Cited by 3 publications

References 72 publications

XTRACT - Standardised protocols for automated tractography in the human and macaque brain

XTRACT - Standardised protocols for automated tractography in the human and macaque brain

MEBRAINS 1.0: a new population-based macaque atlas

Cross-species functional alignment reveals evolutionary hierarchy within the connectome

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