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Metabolic organization of macaque visual cortex reflects visual field topography and perceptual specialization.

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Paper

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The authors' code

Shell · 65 lines · 2.3 KB · no license

  1. #!/bin/bash
  3. # Usage: registerRetino.sh <target_image> [<moving_image>] [<functional_map>]
  5. # Assign input arguments to variables
  6. TARGET_IMAGE=${1:-MPRAGE_SS.nii.gz}
  7. MOVING_IMAGE=${2:-NMT_v2.0_sym_SS.nii.gz}
  8. FUNCTIONAL_MAP=${3:-AvgRetino_NMT2.0sym.nii.gz}
  10. # Define downsampled versions
  11. DOWNSAMPLED_TARGET="downsampled_target.nii.gz"
  12. DOWNSAMPLED_MOVING="downsampled_moving.nii.gz"
  14. # Clean up old outputs to avoid file conflicts
  15. rm -rf step1 step2 step3 step4 step5 AvgRetino_syn2fixed.nii.gz
  17. # Create directories for intermediate files
  18. mkdir -p step1 step2 step3 step4 step5
  20. # Step 1: Downsample both the moving and fixed images to match the resolution of the functional map (1 1 1 mm)
  21. 3dresample -overwrite -dxyz 1 1 1 -prefix step1/$DOWNSAMPLED_TARGET -input $TARGET_IMAGE
  22. 3dresample -overwrite -dxyz 1 1 1 -prefix step1/$DOWNSAMPLED_MOVING -input $MOVING_IMAGE
  24. # From here on out, fixed and moving are the downsampled versions
  25. FIXED="step1/$DOWNSAMPLED_TARGET"
  26. MOVING="step1/$DOWNSAMPLED_MOVING"
  28. # Step 2: Use flirt to register the moving image to the fixed image
  29. flirt -in $MOVING \
  30. -ref $FIXED \
  31. -out step2/moving_flirt2fixed.nii.gz \
  32. -omat step2/moving_flirt2fixed.mat \
  33. -bins 256 -cost corratio \
  34. -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -dof 6 \
  35. -interp trilinear
  37. # Step 3: Runs antsRegistration to register the flirted moving image to the fixed image
  38. antsRegistrationSyN.sh -f $FIXED \
  39. -m step2/moving_flirt2fixed.nii.gz \
  40. -d 3 -o step3/moving_syn2fixed -n 4
  42. # Step 4: Resample the functional map to the moving image
  43. 3dresample -overwrite -master $MOVING -prefix step4/AvgRetino_resamp.nii.gz -input $FUNCTIONAL_MAP
  45. # Step 5: Applies the flirt transform to the resampled functional map using NN interpolation
  46. flirt -in step4/AvgRetino_resamp.nii.gz \
  47. -applyxfm \
  48. -init step2/moving_flirt2fixed.mat \
  49. -out step5/AvgRetino_flirt2moving.nii.gz \
  50. -paddingsize 0.0 -interp nearestneighbour \
  51. -ref $FIXED
  53. # Step 6: Applies ANTs transform to the functional map post flirt transform
  54. antsApplyTransforms \
  55. -e 3 \
  56. --interpolation NearestNeighbor \
  57. -i step5/AvgRetino_flirt2moving.nii.gz \
  58. -r $FIXED \
  59. -t step3/moving_syn2fixed1Warp.nii.gz \
  60. -t step3/moving_syn2fixed0GenericAffine.mat \
  61. -o AvgRetino_syn2fixed.nii.gz
  63. # Step 7: Copy attributes from original dataset
  64. 3drefit -copyaux $FUNCTIONAL_MAP AvgRetino_syn2fixed.nii.gz

registerRetino.sh at commit 1f99b21, no license · at the source

Overview

Authors: Hiroki Oishi1,2,3,4, Vladimir K Berezovskii5, Margaret S Livingstone5, Kevin S Weiner1,6,7, Michael J Arcaro8
ORCID iDs: Hiroki Oishi
  1. Department of Psychology, University of California, Berkeley, California, United States of America
  2. Division of Sensory and Cognitive Brain Mapping, Department of System Neuroscience, National Institute for Physiological Sciences, Okazaki, Aichi, Japan
  3. Graduate Institute for Advanced Studies, SOKENDAI, Hayama, Kanagawa, Japan
  4. Core for Spin Life Sciences, Okazaki Collaborative Platform, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
  5. Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, United States of America
  6. Department of Neuroscience, University of California, Berkeley, California, United States of America
  7. Helen Wills Neuroscience Institute, University of California, Berkeley, California, United States of America
  8. Department of Psychology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
Institutions: National Institutes of Natural Sciences (Japan); The Graduate University for Advanced Studies, SOKENDAI (Japan); National Institute for Physiological Sciences (Japan); University of California, Berkeley (United States); Harvard University (United States); University of Pennsylvania (United States)
Journal: PLoS biology, volume 24, issue 6, article e3003847
Dates: received 17 October 2025; accepted 27 May 2026; published online 8 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pbio.3003847 · PMID 42258495 · PMCID PMC13286273 · OpenAlex W7163924933
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: non-human primate (organism)
Methods: Connectivity, Statistics, Preprocessing, fMRI & imaging
MeSH: Visual Cortex*, Visual Fields*, Visual Perception*, Animals, Brain Mapping, Electron Transport Complex IV, Female, Macaca mulatta, Magnetic Resonance Imaging, Male, Photic Stimulation, Visual Pathways (* major topic)
Topic: Face Recognition and Perception (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: National Science Foundation (NSF CAREER 204225); Japan Society for the Promotion of Science; Whitehall Foundation; National Institutes of Health (P30EY12196, EY16187); Brain and Behavior Research Foundation (NARSAD 30738); Toyobo Biotechnology Foundation
Citations: not cited yet (Europe PMC); 60 references in the paper

Abstract

Neural activity depends on energy metabolism, yet the extent to which regional variation in cortical metabolic architecture reflects the functional and perceptual demands of visual processing remains unclear. In the primate visual system, retinotopic eccentricity, the topographic mapping of visual space relative to gaze, provides a large-scale organizational axis along which spatial resolution and selectivity for behaviorally relevant visual categories vary systematically. Here, we tested whether cortical metabolic architecture reflects this axis by aligning in vivo fMRI maps of eccentricity and visual category selectivity with ex vivo cytochrome oxidase (CO) histology, a marker of oxidative metabolism, in macaque visual cortex. We found that the middle lateral (ML) face-selective region, which is biased toward central vision, exhibited higher CO intensity than the lateral place patch (LPP), a scene-selective region biased toward peripheral vision. More broadly, CO intensity covaried with eccentricity within both ML and LPP and across occipitotemporal visual cortex, though eccentricity only partially accounted for the elevated CO in ML. These findings reveal a close correspondence between cortical metabolic architecture and retinotopic organization, suggesting that the distribution of cortical metabolic resources is shaped by both visual field organization and the processing demands of perceptual specialization.

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

Repository

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

mikearcaro/brainmaps

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 1f99b211b9dc079c61c1b900928ddcfde7dcb13f, 22 May 2025
Languages: Shell (1)
Size: 29 files, 1 script
Software Heritage: not archived
Found in: the text, “Creating and projecting (i) probabilistic face a”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: AFNI (1 file), ANTs (1 file), FSL (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
2 files
At the source: github.com/mikearcaro/BrainMaps/tree/main/Macaque/Retinotopy

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;
  • 1 script, 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

Datasets cited

  • osf:gjbmd, at OSF; found in the text, “CO architecture differs between face- and…”

Data Availability

All CO histological sections, along with the aligned face and place patches and visual ROIs, are publicly available in the repository (https://osf.io/gjbmd/). This repository also contains the codes for generating the plots presented in the figures.

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 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 12 MeSH terms, 6 funders, 60 references.

Cite

This paper

Oishi, H., Berezovskii, V. K., Livingstone, M. S., Weiner, K. S., & Arcaro, M. J. (2026). Metabolic organization of macaque visual cortex reflects visual field topography and perceptual specialization. PLoS biology, 24(6), e3003847. https://doi.org/10.1371/journal.pbio.3003847

BibTeX

@article{oishi2026metabolic,
author = {Oishi, Hiroki and Berezovskii, Vladimir K and Livingstone, Margaret S and Weiner, Kevin S and Arcaro, Michael J},
title = {{Metabolic organization of macaque visual cortex reflects visual field topography and perceptual specialization}},
journal = {PLoS biology},
year = {2026},
month = jun,
volume = {24},
number = {6},
pages = {e3003847},
publisher = {PLOS},
issn = {1544-9173},
doi = {10.1371/journal.pbio.3003847},
url = {https://doi.org/10.1371/journal.pbio.3003847},
pmid = {42258495},
pmcid = {PMC13286273}
}

RIS

TY - JOUR
AU - Oishi, Hiroki
AU - Berezovskii, Vladimir K
AU - Livingstone, Margaret S
AU - Weiner, Kevin S
AU - Arcaro, Michael J
TI - Metabolic organization of macaque visual cortex reflects visual field topography and perceptual specialization
T2 - PLoS biology
J2 - PLoS Biol
PY - 2026
DA - 2026/06/08
VL - 24
IS - 6
SP - e3003847
SN - 1544-9173
PB - PLOS
DO - 10.1371/journal.pbio.3003847
UR - https://doi.org/10.1371/journal.pbio.3003847
LA - en
ER -

CSL-JSON

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"container-title-short": "PLoS Biol",
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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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