Brain activity, disruption and connectivity comparisons identify origins of human metacognition in other primates.
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] § 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] § 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] § 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] § 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
- #!/usr/bin/env bash
- set -e # stop immediately on error
- umask u+rw,g+rw # give group read/write permissions to all new files
- # A wrapper to preprocess macaque structural images, looping over subjects.
- # 1. brain extraction
- # 2. bias correction
- # 3. reference registration
- # These steps are dependent on each other and could therefore be repeated for
- # the best results.
- #
- # Please edit the hard-coded folder definitions and the <subjList>
- # retrieve directory of this script
- scriptDir="$(cd "$( dirname ${BASH_SOURCE[0]} )" && pwd)"
- # find the path to MrCat script library
- [[ -z $MRCATDIR ]] && export MRCATDIR=$(cd $scriptDir/.. && pwd)
- # MRCATDIR="$HOME/scratch/MrCat-dev"
- # MRCATDIR="$HOME/code/MrCat-dev"
- # in this example the subject data is also in the scriptDir
- studyDir=$scriptDir
- # space delineated list of subjects
- subjList="example_data"
- # determine if this script is run locally or on the jalapeno cluster
- cmd="echo" # by default: send command to standard output
- [[ $OSTYPE == "linux-gnu" ]] && cmd="fsl_sub -q short.q -N structmac" # when on linux: submit the job to the jalapeno cluster
- [[ $OSTYPE == "darwin"* ]] && cmd="" # when on a Mac: run locally
- # loop over subjects
- for subj in $subjList ; do
- # preprocess the structural image
- $cmd sh $scriptDir/struct_macaque.sh \
- --all \
- --subjdir=$studyDir/$subj \
- --structimg=$studyDir/$subj/struct/struct \
- --refspace=F99 \
- --refimg=$MRCATDIR/data/macaque/F99/McLaren
- done
wrapper_struct_macaque.sh at commit f86d4e1, under BSD-3-Clause · at the source
Overview
- Laboratory for Imagination and Executive Functions, RIKEN Center for Brain Science,Wako, Japan
- Department of Experimental Psychology, University of Oxford,Oxford, UK
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford,Oxford, UK
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen,Nijmegen, the Netherlands
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/
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
f86d4e14e1ba7aad44dcc3947931b432d46ac52f, 18 November 2021Availability: 1 check, the latest on 28 September 2026: the link answers
- 28 September 2026: the link answers
202 files
- core/
Coord2ROI.sh , Shell, 435 lines - core/
ExpandMotionConfounds.m , MATLAB, 45 lines - core/
FixNegVal.sh , Shell, 136 lines - core/
GMM_fdt.m , MATLAB, 370 lines - core/
GMWMborder.sh , Shell, 41 lines - core/
MIGP.m , MATLAB, 211 lines - core/
MIGP_legacy_20170215.m , MATLAB, 101 lines - core/
RobustBiasCorr.sh , Shell, 273 lines, 1 match - core/
Wrapper_phoenix.sh , Shell, 95 lines - core/
addParam.m , MATLAB, 49 lines - core/
add_toolbox.m , MATLAB, 111 lines - core/
ap_calculateCC.m , MATLAB, 86 lines - core/
ap_cluster_dconn.m , MATLAB, 100 lines - core/
ap_rearrangeCC.m , MATLAB, 42 lines - core/
apcluster.m , MATLAB, 269 lines - core/
apclusterK.m , MATLAB, 89 lines - core/
asymmetry.m , MATLAB, 18 lines - core/
bet_macaque.sh , Shell, 433 lines - core/
binarize.m , MATLAB, 70 lines - core/
cifti_open.m , MATLAB, 188 lines - core/
ciftiopen.m , MATLAB, 64 lines - core/
clean_logdir.sh , Shell, 41 lines - core/
cluster_threshold.m , MATLAB, 117 lines - core/
columnentropy.m , MATLAB, 92 lines - core/
conngrads_cc.m , MATLAB, 32 lines - core/
conngrads_dconn.m , MATLAB, 215 lines - core/
conngrads_diff.m , MATLAB, 60 lines - core/
conngrads_eps.m , MATLAB, 79 lines - core/
conngrads_eta2.m , MATLAB, 45 lines - core/
conngrads_euc.m , MATLAB, 32 lines - core/
conngrads_fdt.m , MATLAB, 275 lines - core/
conngrads_gau.m , MATLAB, 27 lines - core/
conngrads_knn.m , MATLAB, 82 lines - core/
conngrads_lap.m , MATLAB, 35 lines - core/
conngrads_proj_prep.m , MATLAB, 59 lines - core/
conngrads_ps.m , MATLAB, 32 lines - core/
conngrads_sim.m , MATLAB, 50 lines - core/
conngrads_sp.m , MATLAB, 53 lines - core/
cosine_similarity.m , MATLAB, 44 lines - core/
create_func_gii.m , MATLAB, 73 lines - core/
create_gifti.m , MATLAB, 171 lines - core/
create_multibrain_vol.m , MATLAB, 73 lines - core/
create_spec_file.m , MATLAB, 57 lines - core/
cut_outlier.sh , Shell, 303 lines - core/
demean.m , MATLAB, 37 lines - core/
dice.m , MATLAB, 30 lines - core/
erase.m , MATLAB, 46 lines - core/
eta_template.m , MATLAB, 55 lines - core/
euclid.m , MATLAB, 53 lines - core/
fisherz.m , MATLAB, 17 lines - core/
get_gifti_type.m , MATLAB, 40 lines - core/
get_jointprobs.m , MATLAB, 30 lines - core/
ggfit.m , MATLAB, 112 lines - core/
glass.m , MATLAB, 228 lines - core/
glass_projection.m , MATLAB, 319 lines - core/
hierarchicalclustering.m , MATLAB, 87 lines - core/
inverse_fisherz.m , MATLAB, 17 lines - core/
islander_borgify.m , MATLAB, 61 lines - core/
islander_colonize.m , MATLAB, 109 lines - core/
jobID.sh , Shell, 9 lines - core/
jointentropy.m , MATLAB, 47 lines - core/
km_calculateCC.m , MATLAB, 83 lines - core/
km_calculateD.m , MATLAB, 115 lines - core/
km_connexityconstraint_v , MATLAB, 117 linesolume.m - core/
km_hierarchyindex.m , MATLAB, 134 lines - core/
km_init.m , MATLAB, 137 lines - core/
km_init_furthest.m , MATLAB, 60 lines - core/
km_init_kdtree.m , MATLAB, 133 lines - core/
km_silhouette.m , MATLAB, 97 lines - core/
km_vi.m , MATLAB, 48 lines - core/
kmeans_dconn.m , MATLAB, 224 lines - core/
kmeans_fast.m , MATLAB, 181 lines - core/
kmeans_fdt.m , MATLAB, 342 lines - core/
line_trendline.m , MATLAB, 11 lines - core/
load_gifti.m , MATLAB, 505 lines - core/
load_gifti_data.m , MATLAB, 67 lines - core/
load_xml.m , MATLAB, 39 lines - core/
log_threshold.m , MATLAB, 88 lines - core/
look_at_moriarty.m , MATLAB, 204 lines - core/
mae.sh , Shell, 109 lines - core/
mahalanobis.m , MATLAB, 37 lines - core/
make_empty_gifti.m , MATLAB, 164 lines - core/
manhattan.m , MATLAB, 40 lines - core/
maskmean.m , MATLAB, 18 lines - core/
maskmean_nonzero.m , MATLAB, 13 lines - core/
mat2dtseries.m , MATLAB, 74 lines - core/
moriarty2.m , MATLAB, 178 lines - core/
moriarty_ggm.m , MATLAB, 106 lines - core/
multiply_fdt.m , MATLAB, 199 lines - core/
mutualinformation.m , MATLAB, 50 lines - core/
mygfilter.m , MATLAB, 57 lines - core/
normalise.m , MATLAB, 45 lines - core/
normalize0.m , MATLAB, 22 lines - core/
normalize1.m , MATLAB, 74 lines - core/
partialcorrmatrix.m , MATLAB, 123 lines - core/
perm_results.m , MATLAB, 118 lines - core/
plot_trendline.m , MATLAB, 27 lines - core/
preferenceRange.m , MATLAB, 99 lines - core/
quick_plot.m , MATLAB, 47 lines - core/
randomize_vector.m , MATLAB, 26 lines - core/
read_avw_multi.m , MATLAB, 148 lines - core/
read_fsl_design_matrix.m , MATLAB, 55 lines - core/
readimgfile.m , MATLAB, 266 lines - core/
registerT1wCT.sh , Shell, 493 lines - core/
register_EPI_T1.sh , Shell, 401 lines - core/
regress_out.m , MATLAB, 72 lines - core/
replacenan.m , MATLAB, 9 lines - core/
rmse.sh , Shell, 112 lines - core/
robustfov_macaque.sh , Shell, 206 lines - core/
rotbvecs.sh , Shell, 126 lines - core/
run_fixed.sh , Shell, 101 lines - core/
run_flex.sh , Shell, 198 lines - core/
save_gifti.m , MATLAB, 183 lines - core/
saveimgfile.m , MATLAB, 118 lines - core/
scatter_trendline.m , MATLAB, 27 lines - core/
sm_compare2template.m , MATLAB, 161 lines - core/
sm_comparegroups.m , MATLAB, 275 lines - core/
sm_findpermutations.m , MATLAB, 72 lines - core/
smape.sh , Shell, 132 lines - core/
sort_CC_matrix.m , MATLAB, 99 lines - core/
sortmatrixrows.m , MATLAB, 5 lines - core/
spider_regression.m , MATLAB, 85 lines, 1 match - core/
spider_wedge.m , MATLAB, 738 lines - core/
ss_svds.m , MATLAB, 46 lines - core/
strcontain.m , MATLAB, 27 lines - core/
strerase.m , MATLAB, 23 lines - core/
strreplace.m , MATLAB, 24 lines - core/
struct_macaque.sh , Shell, 595 lines - core/
surf_cog.m , MATLAB, 168 lines - core/
surf_crosscorr.m , MATLAB, 77 lines - core/
swapdims.sh , Shell, 76 lines - core/
threshold.m , MATLAB, 17 lines - core/
tract3D.m , MATLAB, 733 lines - core/
transformCoordANTs.sh , Shell, 147 lines - core/
uthreshold.m , MATLAB, 15 lines - pipelines/
ex_vivo/ , MATLAB, 14 linesROB_scripts/ load_agilant.m - pipelines/
ex_vivo/ , MATLAB, 36 linesROB_scripts/ load_fid.m - pipelines/
ex_vivo/ , MATLAB, 31 linesROB_scripts/ load_fid_hdr.m - pipelines/
ex_vivo/ , MATLAB, 125 linesROB_scripts/ readprocpar.m - pipelines/
rfmri_macaque/ , Shell, 126 linesrsn_biascorr.sh - pipelines/
rfmri_macaque/ , MATLAB, 248 linesrsn_cleanComp.m - pipelines/
rfmri_macaque/ , Shell, 512 linesrsn_cleanComp.sh - pipelines/
rfmri_macaque/ , MATLAB, 134 lines, 1 matchrsn_cleanCompSimple.m - pipelines/
rfmri_macaque/ , MATLAB, 64 linesrsn_cleanPca.m - pipelines/
rfmri_macaque/ , MATLAB, 113 linesrsn_cleanVariance.m - pipelines/
rfmri_macaque/ , MATLAB, 51 linesrsn_cleanVariancePca.m - pipelines/
rfmri_macaque/ , MATLAB, 159 linesrsn_decomp.m - pipelines/
rfmri_macaque/ , MATLAB, 57 linesrsn_demean.m - pipelines/
rfmri_macaque/ , MATLAB, 98 linesrsn_detrend.m - pipelines/
rfmri_macaque/ , Shell, 128 linesrsn_discardFirstVols.sh - pipelines/
rfmri_macaque/ , MATLAB, 483 linesrsn_filter.m - pipelines/
rfmri_macaque/ , MATLAB, 174 linesrsn_fixOutlier.m - pipelines/
rfmri_macaque/ , Shell, 188 linesrsn_motionCorr.sh - pipelines/
rfmri_macaque/ , MATLAB, 65 linesrsn_normalise.m - pipelines/
rfmri_macaque/ , Shell, 464 linesrsn_outlier.sh - pipelines/
rfmri_macaque/ , Shell, 692 linesrsn_pipeline.sh - pipelines/
rfmri_macaque/ , Shell, 158 linesrsn_registerFunc2Struct. sh - pipelines/
rfmri_macaque/ , Shell, 120 linesrsn_reorient.sh - pipelines/
rfmri_macaque/ , Shell, 66 linesrsn_swapdim.sh - pipelines/
rfmri_macaque/ , Shell, 288 linesrsn_vol2surf.sh - pipelines/
templating/ , Shell, 33 linesWrapper_templating.sh - pipelines/
templating/ , Shell, 542 linestemplating.sh - pipelines/
wrapper_register_EPI_T1. , Shell, 88 linessh - pipelines/
wrapper_struct_macaque.s , Shell, 45 lines, 1 matchh - pubs/
amygdala-ACC-TUS/ , MATLAB, 1,293 linesAnalyseFingerprint.m - pubs/
amygdala-ACC-TUS/ , Shell, 367 linesConnHeatmap.sh - pubs/
amygdala-ACC-TUS/ , MATLAB, 162 linesPimpIntensityPlots.m - pubs/
amygdala-ACC-TUS/ , Shell, 43 linesinstructions/ sourceConfig.sh - pubs/
offlineTUS/ , MATLAB, 405 linesAnalyseCompartmentVarian ce.m - pubs/
offlineTUS/ , MATLAB, 1,176 linesAnalyseFingerprint.m - pubs/
offlineTUS/ , Shell, 87 linesAverageDenseConn.sh - pubs/
offlineTUS/ , Shell, 167 linesAverageMap.sh - pubs/
offlineTUS/ , Shell, 53 linesCompareDenseConn.sh - pubs/
offlineTUS/ , Shell, 127 linesCompareMaps.sh - pubs/
offlineTUS/ , Shell, 140 linesCompartmentComponents.sh - pubs/
offlineTUS/ , Shell, 160 linesConfoundSeries.sh - pubs/
offlineTUS/ , Shell, 174 linesConfoundStat.sh - pubs/
offlineTUS/ , Shell, 24 linesConvertDCM2NII.sh - pubs/
offlineTUS/ , Shell, 347 linesCreateROI.sh - pubs/
offlineTUS/ , Shell, 159 linesCreateVolLabel.sh - pubs/
offlineTUS/ , Shell, 97 linesDenseConn.sh - pubs/
offlineTUS/ , Shell, 288 linesExtractFingerprint.sh - pubs/
offlineTUS/ , Shell, 122 linesGenericRunProc.sh - pubs/
offlineTUS/ , Shell, 130 linesInitFunc.sh - pubs/
offlineTUS/ , Shell, 293 linesMergeFunc.sh - pubs/
offlineTUS/ , MATLAB, 209 linesPimpIntensityPlots.m - pubs/
offlineTUS/ , MATLAB, 304 linesPimpThermalPlots.m - pubs/
offlineTUS/ , MATLAB, 20 linesPlotSMAPE.m - pubs/
offlineTUS/ , Shell, 183 linesProcFunc.sh - pubs/
offlineTUS/ , Shell, 56 linesProcStruct.sh - pubs/
offlineTUS/ , MATLAB, 121 linesQuantifyGlobalConn.m - pubs/
offlineTUS/ , Shell, 284 linesQuantifyTimeSeries.sh - pubs/
offlineTUS/ , MATLAB, 132 linesRegressDenseConn.m - pubs/
offlineTUS/ , Shell, 88 linesScaleDenseConn.sh - pubs/
offlineTUS/ , Shell, 341 linesSeedConn.sh - pubs/
offlineTUS/ , Shell, 69 linesSetupInstruct.sh - pubs/
offlineTUS/ , Shell, 8 linescoordWarp.sh - pubs/
offlineTUS/ , Shell, 43 linesinstructions/ sourceConfig.sh - setupMrCat.m, MATLAB, 18 lines
- setupMrCat.sh, Shell, 139 lines
- LICENSE.md, License, 5 lines
- README.md, Text, 9 lines
neurodata.riken.jp
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 206)
- 28 September 2026: the link answers (HTTP 206)
Code availability
Codes that support the findings of this study are available via RIKEN CBS Data Sharing Platform at https://
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://
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://
BibTeX
@article{miyamoto2026bra
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/
url = {https://
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/
VL - 10
IS - 8
SP - 1557
EP - 1578
SN - 2397-3374
PB - Nature Portfolio
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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"container-title": "Nature human behaviour",
"author": [
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"family": "Miyamoto",
"given": "Kentaro"
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{
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{
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}
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"container-title-short":
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"URL": "https://
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"issued": {
"date-parts": [
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18
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]
}
}
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