OSCR

Development of a 24-channel 3T phased-array coil for fMRI in awake monkeys: Mitigating spatiotemporal artifacts in ferumoxytol-weighted functional connectivity estimation.

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The authors' code

Shell · 4 lines · 161 B · no license

  1. export CARET7DIR=/mnt/pub/devel/workbench/release/1.5.0
  2. export HCPPIPEDIR=/mnt/pub/devel/NHPHCPPipeline
  3. export FREESURFER_HOME=/usr/local/freesurfer-v5.3.0-HCP

settings.sh at commit 9363e10, no license · at the source

Overview

Authors: Joonas A Autio1,2, Atsushi Yoshida1,3, Yoshihiko Kawabata4, Masahiro Ohno1, Kantaro Nishigori1,5, Takayuki Ose1, Stephen M Smith6, David C Van Essen2, Matthew F Glasser2,7, Takuya Hayashi1,8,9
ORCID iDs: Joonas A Autio, Takuya Hayashi
  1. Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
  2. Department of Neuroscience, Washington University Medical School, St Louis, MO, United States
  3. Systems Neuroscience Laboratory, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, Japan
  4. Takashima Seisakusho Co., Ltd, Tokyo, Japan
  5. Sumitomo Pharma Co., Ltd, Osaka, Japan
  6. Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom
  7. Department of Radiology, Washington University Medical School, St Louis, MO, United States
  8. Department of Brain Connectomics, Kyoto University Graduate School of Medicine, Kyoto, Japan
  9. Section of Brain Function Information, National Institute for Physiological Sciences, Okazaki, Japan
Institutions: RIKEN Center for Biosystems Dynamics Research (Japan); Hokkaido University (Japan); University of Oxford (United Kingdom); Wellcome Centre for Integrative Neuroimaging (United Kingdom); Washington University in St. Louis (United States); Kyoto University (Japan)
Journal: Imaging neuroscience (Cambridge, Mass.), volume 4, article IMAG.a.1354
Dates: received 25 December 2024; accepted 3 July 2026; published online 3 September 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1162/imag.a.1354 · PMID 42699021 · PMCID PMC13543443 · OpenAlex W4409727531
Open access: diamond, a free copy (OpenAlex)
Preprint: doi:10.1101/2025.04.15.648822
Status: code verified
Categories: fMRI (modality), human (organism), non-human primate (organism), cellular / molecular (subfield)
Methods: Connectivity, Smoothing, state filtering, decompositions, fMRI & imaging, Physiology & signal measures, Preprocessing
Keywords: macaque, awake, RF coil, fMRI, ferumoxytol
MeSH: Brain*, Ferrosoferric Oxide*, Magnetic Resonance Imaging*, Animals, Artifacts, Brain Mapping, Connectome, Contrast Media, Image Processing, Computer-Assisted, Macaca mulatta, Wakefulness (* major topic)
Topic: Functional Brain Connectivity Studies (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: NIMH NIH HHS (UM1 MH130981, R01 MH060974)
Citations: not cited yet (Europe PMC); 90 references in the paper

Abstract

Functional magnetic resonance imaging (fMRI) of awake macaque monkeys holds promise for advancing our understanding of primate brain organization, including humans. However, estimating functional connectivity in awake animals is challenging due to the limited duration of imaging sessions and the relatively low sensitivity to neural activity. To overcome these challenges, we developed a 24-channel 3T receive radiofrequency (RF) coil optimized for parallel imaging of awake macaques. This enabled the acquisition of cross-plane and in-plane accelerated ferumoxytol-weighted resting-state fMRI. The Human Connectome Project-style data processing pipelines were adapted to address the unique preprocessing demands of cerebral blood volume-weighted (CBVw) imaging, including motion correction, functional-to-structural image co-registration, and training a multi-run independent component analysis-based X-noiseifier (ICA-FIX) classifier for removal of structured artifacts. Our CBVw fMRI approach resulted in an elevated contrast-to-noise ratio compared with blood oxygenation level-dependent (BOLD) imaging in anesthetized macaques. However, structured imaging artifacts still contributed more variance to the functional timeseries than neural activity. By applying the ICA-FIX classifier, we achieved highly reproducible parcellated functional connectivity at the single-subject level, with test–retest matrix correlations and subject identification accuracy comparable with those observed in humans. At the group level, we identified dense functional networks with spatial features homologous to those observed in humans. The developed RF receive coil, image acquisition protocols, and data analysis pipelines are publicly available, providing the broader scientific community with tools to leverage these advances for further research.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

RIKEN-BCIL/bcil

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 9363e1021797cd6ee094293813383f5817513875, 18 August 2026
Languages: Shell (3), R (3), JavaScript (3), MATLAB (2)
Size: 91 files, 11 scripts
Software Heritage: not archived
Found in: the text, “Adapting NHP–HCP data analysis pipelines for CBV”
Holds: README, documentation
Not found: license file, CITATION.cff, environment file, tests, continuous integration
Tools: FSL (2 files), ggplot2 (2 files), HCP Pipelines (2 files), cifti-matlab (1 file), FreeSurfer (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
12 files
At the source: github.com/RIKEN-BCIL/bcil

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 11 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data and Code Availability

The 24-channel RF receive coil for awake macaque monkeys is commercially available via Rogue Research, Montreal, Canada https://www.rogue-research.com/, produced by Takashima Seisakusho Co. Ltd. Tokyo, Japan.

The imaging protocols are available at https://brainminds-beyond.riken.jp/hcp-nhp-protocol. The NHP version pipelines is now merged with HCP pipeline and available at https://github.com/Washington-University/HCPpipelines.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 3, 28 September 2026

  • Authors: added Joonas A Autio (0000-0002-2232-9259); removed Joonas A Autio

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 10 authors, 5 keywords, 11 MeSH terms, 1 funder, 88 references.

Cite

This paper

Autio, J. A., Yoshida, A., Kawabata, Y., Ohno, M., Nishigori, K., Ose, T., Smith, S. M., Van Essen, D. C., Glasser, M. F., & Hayashi, T. (2026). Development of a 24-channel 3T phased-array coil for fMRI in awake monkeys: Mitigating spatiotemporal artifacts in ferumoxytol-weighted functional connectivity estimation. Imaging neuroscience (Cambridge, Mass.), 4, IMAG.a.1354. https://doi.org/10.1162/imag.a.1354

BibTeX

@article{autio2026development,
author = {Autio, Joonas A and Yoshida, Atsushi and Kawabata, Yoshihiko and Ohno, Masahiro and Nishigori, Kantaro and Ose, Takayuki and Smith, Stephen M and Van Essen, David C and Glasser, Matthew F and Hayashi, Takuya},
title = {{Development of a 24-channel 3T phased-array coil for fMRI in awake monkeys: Mitigating spatiotemporal artifacts in ferumoxytol-weighted functional connectivity estimation}},
journal = {Imaging neuroscience (Cambridge, Mass.)},
year = {2026},
month = sep,
volume = {4},
pages = {IMAG.a.1354},
publisher = {MIT Press},
issn = {2837-6056},
doi = {10.1162/imag.a.1354},
url = {https://doi.org/10.1162/imag.a.1354},
pmid = {42699021},
pmcid = {PMC13543443}
}

RIS

TY - JOUR
AU - Autio, Joonas A
AU - Yoshida, Atsushi
AU - Kawabata, Yoshihiko
AU - Ohno, Masahiro
AU - Nishigori, Kantaro
AU - Ose, Takayuki
AU - Smith, Stephen M
AU - Van Essen, David C
AU - Glasser, Matthew F
AU - Hayashi, Takuya
TI - Development of a 24-channel 3T phased-array coil for fMRI in awake monkeys: Mitigating spatiotemporal artifacts in ferumoxytol-weighted functional connectivity estimation
T2 - Imaging neuroscience (Cambridge, Mass.)
J2 - Imaging Neurosci (Camb)
PY - 2026
DA - 2026/09/03
VL - 4
SP - IMAG.a.1354
SN - 2837-6056
PB - MIT Press
DO - 10.1162/imag.a.1354
UR - https://doi.org/10.1162/imag.a.1354
LA - en
ER -

CSL-JSON

{
"id": "10.1162/imag.a.1354",
"type": "article-journal",
"title": "Development of a 24-channel 3T phased-array coil for fMRI in awake monkeys: Mitigating spatiotemporal artifacts in ferumoxytol-weighted functional connectivity estimation",
"container-title": "Imaging neuroscience (Cambridge, Mass.)",
"author": [
{
"family": "Autio",
"given": "Joonas A"
},
{
"family": "Yoshida",
"given": "Atsushi"
},
{
"family": "Kawabata",
"given": "Yoshihiko"
},
{
"family": "Ohno",
"given": "Masahiro"
},
{
"family": "Nishigori",
"given": "Kantaro"
},
{
"family": "Ose",
"given": "Takayuki"
},
{
"family": "Smith",
"given": "Stephen M"
},
{
"family": "Van Essen",
"given": "David C"
},
{
"family": "Glasser",
"given": "Matthew F"
},
{
"family": "Hayashi",
"given": "Takuya"
}
],
"container-title-short": "Imaging Neurosci (Camb)",
"volume": "4",
"page": "IMAG.a.1354",
"DOI": "10.1162/imag.a.1354",
"PMID": "42699021",
"PMCID": "PMC13543443",
"ISSN": "2837-6056",
"publisher": "MIT Press",
"URL": "https://doi.org/10.1162/imag.a.1354",
"language": "en",
"issued": {
"date-parts": [
[
2026,
9,
3
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.21203/rs.3.rs-9326213/v1 [code]
Multi-task fMRI outperforms resting-state fMRI for revealing task-invariant organization of the human brain
Journal: Research Square (preprint)
In common: FreeSurfer, FSL, fMRI, 13 references
[2] doi:10.64898/2026.03.09.710558 [code]
Multi-task fMRI outperforms resting-state fMRI for revealing task-invariant organization of the human brain
Journal: bioRxiv (preprint)
In common: FreeSurfer, FSL, fMRI, 13 references
[3] doi:10.1162/netn.a.547 [code]
An evaluation of the efficacy of single-echo and multi-echo fMRI denoising strategies.
Journal: Network neuroscience (Cambridge, Mass.)
In common: FreeSurfer, FSL, fMRI, 10 references
[4] doi:10.1038/s41562-026-02473-w [code]
Brain activity, disruption and connectivity comparisons identify origins of human metacognition in other primates.
Journal: Nature human behaviour
In common: HCP Pipelines, cifti-matlab, FreeSurfer, 1 other tool, non-human primate, 3 references
[5] doi:10.1002/advs.202523009 [code]
Personalized Network-Guided Neuromodulation Enhances Human Working Memory.
Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)
In common: cifti-matlab, FreeSurfer, FSL, 1 other tool, 5 references
[6] doi:10.1002/hbm.70621 [code]
Optimising 7T-fMRI for Imaging Regions of Magnetic Susceptibility.
Journal: Human brain mapping
In common: FSL, fMRI, 7 references
[7] doi:10.1162/imag.a.1198 [code]
MEPrep: A robust pipeline for multi-echo fMRI denoising and preprocessing.
Journal: Imaging neuroscience (Cambridge, Mass.)
In common: FreeSurfer, FSL, fMRI, 6 references
[8] doi:10.1038/s41467-026-71270-w [code]
Spatiotemporal dynamics of the human cortical functional hierarchy across the lifespan.
Journal: Nature communications
In common: HCP Pipelines, FreeSurfer, FSL, 1 other tool, fMRI, 2 references
[9] doi:10.1162/imag.a.1222 [code]
Network-based near-scalp personalized brain stimulation targets.
Journal: Imaging neuroscience (Cambridge, Mass.)
In common: FreeSurfer, FSL, 6 references
[10] doi:10.1162/imag.a.1350 [code]
Clarifying and extending permutation tests on brain map correspondence through mixed-effects modeling.
Journal: Imaging neuroscience (Cambridge, Mass.)
In common: FreeSurfer, 7 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.