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Brain activity, disruption and connectivity comparisons identify origins of human metacognition in other primates.

Code ↔ Paper

4 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 4 matches · 3 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Quantification and statistical analysis › Reconstruction and preprocessing of MRI data ↔ pipelines/wrapper_struct_macaque.sh, the whole file · a weak match · score 0.71 · McLaren, MrCat, brain extraction, Library, bias, echo
  2. [2] § Methods › Quantification and statistical analysis › Reconstruction and preprocessing of MRI data ↔ core/RobustBiasCorr.sh, lines 206–273 · score 0.65 · bias field correction, brain extraction, FLIRT, Iterative, BET, FSL
  3. [3] § Methods › Quantification and statistical analysis › Behavioural analysis ↔ core/spider_regression.m, the whole file · a weak match · score 0.52 · Independent variables, model, beta, zero, regression
  4. [4] § Methods › Quantification and statistical analysis › Reconstruction and preprocessing of MRI data ↔ pipelines/rfmri_macaque/rsn_cleanCompSimple.m, the whole file · a weak match · score 0.52 · general linear models, GLMs, filtered, component, volume, regressors

Paper

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

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The authors' code

Shell · 45 lines · 1.4 KB · BSD-3-Clause · 1 match

  1. #!/usr/bin/env bash
  2. set -e # stop immediately on error
  3. umask u+rw,g+rw # give group read/write permissions to all new files
  4. # A wrapper to preprocess macaque structural images, looping over subjects.
  5. # 1. brain extraction
  6. # 2. bias correction
  7. # 3. reference registration
  8. # These steps are dependent on each other and could therefore be repeated for
  9. # the best results.
  10. #
  11. # Please edit the hard-coded folder definitions and the <subjList>
  12. # retrieve directory of this script
  13. scriptDir="$(cd "$( dirname ${BASH_SOURCE[0]} )" && pwd)"
  14. # find the path to MrCat script library
  15. [[ -z $MRCATDIR ]] && export MRCATDIR=$(cd $scriptDir/.. && pwd)
  16. # MRCATDIR="$HOME/scratch/MrCat-dev"
  17. # MRCATDIR="$HOME/code/MrCat-dev"
  18. # in this example the subject data is also in the scriptDir
  19. studyDir=$scriptDir
  20. # space delineated list of subjects
  21. subjList="example_data"
  22. # determine if this script is run locally or on the jalapeno cluster
  23. cmd="echo" # by default: send command to standard output
  24. [[ $OSTYPE == "linux-gnu" ]] && cmd="fsl_sub -q short.q -N structmac" # when on linux: submit the job to the jalapeno cluster
  25. [[ $OSTYPE == "darwin"* ]] && cmd="" # when on a Mac: run locally
  26. # loop over subjects
  27. for subj in $subjList ; do
  28. # preprocess the structural image
  29. $cmd sh $scriptDir/struct_macaque.sh \
  30. --all \
  31. --subjdir=$studyDir/$subj \
  32. --structimg=$studyDir/$subj/struct/struct \
  33. --refspace=F99 \
  34. --refimg=$MRCATDIR/data/macaque/F99/McLaren
  35. done

wrapper_struct_macaque.sh at commit f86d4e1, under BSD-3-Clause · at the source

Overview

Authors: Kentaro Miyamoto1,2, Simone D’Ambrogio2, Caroline Harbison2, Nicole Eichert3, Urs Schüffelgen2, Andrew Emberton2, Jerome Sallet2, Rogier B. Mars3,4, Nima Khalighinejad2, Matthew FS Rushworth2
  1. Laboratory for Imagination and Executive Functions, RIKEN Center for Brain Science,Wako, Japan
  2. Department of Experimental Psychology, University of Oxford,Oxford, UK
  3. Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford,Oxford, UK
  4. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen,Nijmegen, the Netherlands
Institutions: RIKEN Center for Brain Science (Japan); University of Oxford (United Kingdom); Radboud University Nijmegen (Netherlands)
Journal: Nature human behaviour, volume 10, issue 8, pages 1557-1578
Dates: received 29 August 2025; accepted 9 April 2026; published online 18 May 2026; in print 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41562-026-02473-w · PMID 42151552 · PMCID PMC13485697 · OpenAlex W7161571958
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), non-human primate (organism), cognitive (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Connectivity, fMRI & imaging
Keywords: Decision, Consciousness
MeSH: Metacognition*, Prefrontal Cortex*, Adult, Animals, Biological Evolution, Brain Mapping, Female, Humans, Macaca mulatta, Magnetic Resonance Imaging, Male (* major topic)
Topic: Memory and Neural Mechanisms (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: Japan Society for the Promotion of Science (JP25H00583, JP25K21988 and JP23H03843); Japan Agency for Medical Research and Development (JP24wm0525034 and JP23wm0625001); Wellcome Trust (Wellcome) (222799/Z/21/Z, 221794/Z/20/Z); RCUK | Biotechnology and Biological Sciences Research Council (BBSRC) (BB/W008947/1, BB/W003392/1); UK Medical Research Council (MR/P024955/1)
Citations: cited by 1 paper (Europe PMC); 69 references in the paper

Abstract

Planning requires anticipating the environmental contingencies that we will encounter and also our own future behaviour in those scenarios. The evolutionary origins of such prospective decision simulations have, however, been difficult to investigate. Moreover, in humans, these metacognitive processes are associated with a distinctively human brain region in the anterior lateral prefrontal cortex. Here we demonstrate these capacities in macaques and their neural bases in two complementary patterns of brain activity in different ventrolateral prefrontal areas: areas 45a and 47/12o. We also examine the impact of ultrasonic disruption of each area. We compare behavioural, brain activity and disruption patterns in humans and macaques. Finally, comparative connectional analysis revealed similarities between the conjunction of the two circuits associated with areas 45a and 47/12o in macaques and the human anterior lateral prefrontal area. In combination, the results suggest behavioural and anatomical origins of metacognitive processes that have become especially sophisticated in humans.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.

neuroecology/MrCat

License: BSD-3-Clause
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: f86d4e14e1ba7aad44dcc3947931b432d46ac52f, 18 November 2021
Languages: MATLAB (139), Shell (61)
Size: 254 files, 200 scripts
Software Heritage: not archived
Found in: “Code availability”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: FSL (40 files), Connectome Workbench (18 files), Statistics and Machine Learning Toolbox (17 files), cifti-matlab (11 files), GIfTI library for MATLAB (10 files), export_fig (6 files), FieldTrip (4 files), ANTs (3 files), Image Processing Toolbox (2 files), Tools for NIfTI and ANALYZE image (MATLAB) (2 files), FreeSurfer (1 file), HCP Pipelines (1 file), Signal Processing Toolbox (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
202 files

neurodata.riken.jp

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: the link answers
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 206)
  • 28 September 2026: the link answers (HTTP 206)
At the source: neurodata.riken.jp/

Code availability

Codes that support the findings of this study are available via RIKEN CBS Data Sharing Platform at https://neurodata.riken.jp/ with an identifier (10.60178/cbs.20260313-001) and via GitHub at http://github.com/neuroecology/MrCat.

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

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 200 scripts, each with its path and the digest of its content;
  • 4 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • 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 availability

Data that support the findings of this study are available via RIKEN CBS Data Sharing Platform at https://neurodata.riken.jp/ with an identifier (10.60178/cbs.20260313-001).

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 2, 28 September 2026

  • Publisher: n/a → Nature Portfolio

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 2 keywords, 11 MeSH terms, 5 funders, 66 references.

Cite

This paper

Miyamoto, K., D’Ambrogio, S., Harbison, C., Eichert, N., Schüffelgen, U., Emberton, A., Sallet, J., Mars, R. B., Khalighinejad, N., & Rushworth, M. F. (2026). Brain activity, disruption and connectivity comparisons identify origins of human metacognition in other primates. Nature human behaviour, 10(8), 1557-1578. https://doi.org/10.1038/s41562-026-02473-w

BibTeX

@article{miyamoto2026brain,
author = {Miyamoto, Kentaro and D’Ambrogio, Simone and Harbison, Caroline and Eichert, Nicole and Schüffelgen, Urs and Emberton, Andrew and Sallet, Jerome and Mars, Rogier B. and Khalighinejad, Nima and Rushworth, Matthew FS},
title = {{Brain activity, disruption and connectivity comparisons identify origins of human metacognition in other primates}},
journal = {Nature human behaviour},
year = {2026},
month = may,
volume = {10},
number = {8},
pages = {1557--1578},
publisher = {Nature Portfolio},
issn = {2397-3374},
doi = {10.1038/s41562-026-02473-w},
url = {https://doi.org/10.1038/s41562-026-02473-w},
pmid = {42151552},
pmcid = {PMC13485697}
}

RIS

TY - JOUR
AU - Miyamoto, Kentaro
AU - D’Ambrogio, Simone
AU - Harbison, Caroline
AU - Eichert, Nicole
AU - Schüffelgen, Urs
AU - Emberton, Andrew
AU - Sallet, Jerome
AU - Mars, Rogier B.
AU - Khalighinejad, Nima
AU - Rushworth, Matthew FS
TI - Brain activity, disruption and connectivity comparisons identify origins of human metacognition in other primates
T2 - Nature human behaviour
J2 - Nat Hum Behav
PY - 2026
DA - 2026/05/18
VL - 10
IS - 8
SP - 1557
EP - 1578
SN - 2397-3374
PB - Nature Portfolio
DO - 10.1038/s41562-026-02473-w
UR - https://doi.org/10.1038/s41562-026-02473-w
LA - en
ER -

CSL-JSON

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"type": "article-journal",
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"container-title": "Nature human behaviour",
"author": [
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"family": "Miyamoto",
"given": "Kentaro"
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The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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