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Predicting visual mental imagery: structural and transcriptomic signatures in the human brain.

Code ↔ Paper

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Paper

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The authors' code

MATLAB · 44 lines · 1.2 KB · CC-BY-4.0

  1. load('volumeData.mat');
  2. load('BehaviorData.mat');
  3. significantROIs = significantROIs(significantROIs ~= 47);
  4. GrayVol_ROI = ROI_matrix(:, significantROIs);
  5. behav_vec = BehaviorData.VVIQ;
  6. AgeT1 = BehaviorData.AGE;
  7. eTIVT1 = BehaviorData.eTIV;
  8. RavenT1 = BehaviorData.Raven;
  9. GenderT1 = BehaviorData.Gender;
  10. [r, p] = partialcorr(behav_vec, GrayVol_ROI, [AgeT1, eTIVT1, RavenT1, GenderT1],"Type","Spearman");
  11. Z_values = 0.5 * log((1 + r) ./ (1 - r));
  12. z_mat = Z_values;
  13. z_mat
  15. load('exprMatrixOverall_reconall_148_NEW.mat')
  16. gene_ROI = exprMatrixOverall(significantROIs, :);
  17. numRegions = size(gene_ROI, 1);
  18. numGenes = size(gene_ROI, 2);
  19. numRegions
  20. numGenes
  22. r_values = NaN(numGenes, 1);
  23. p_values = NaN(numGenes, 1);
  25. for g = 1:numGenes
  26. gene_expression = gene_ROI(:, g);
  28. [r_gene, p_gene] = corr(Z_values', gene_expression, 'Type', 'Spearman');
  29. r_values(g) = r_gene;
  30. p_values(g) = p_gene;
  31. end
  33. significant_genes = find(p_values < 0.05 & r_values > 0);
  35. load('probeInformation.mat');
  36. gene_ID = probeInformation.EntrezID(significant_genes);
  37. outfile = 'significant_gene_ids.txt';
  39. fid = fopen(outfile, 'w');
  40. for i = 1:numel(gene_ID)
  41. fprintf(fid, '%d\n', gene_ID(i));
  42. end
  44. fclose(fid);

gene.m, under CC-BY-4.0 · at the source

Overview

Authors: Ruxin Xu1, Dai Zhang2,3, Ke Zhou1, Liqin Zhou1
ORCID iDs: Ruxin Xu, Dai Zhang, Ke Zhou, Liqin Zhou
  1. Beijing Key Laboratory of Applied Experimental Psychology, National Demonstration Center for Experimental Psychology Education (Beijing Normal University), Faculty of Psychology, Beijing Normal University,Beijing, China
  2. Department of Radiology, The Second Affiliated Hospital of Anhui Medical University, No.678 Furong Road,Hefei, Anhui China
  3. Medical Imaging Research Center, Anhui Medical University, No.678 Furong Road,Hefei, Anhui China
Institutions: Beijing Normal University (China); Second Affiliated Hospital of Anhui Medical University (China); Anhui Medical University (China)
Journal: Communications biology, volume 9, issue 1, article 1113
Dates: received 18 November 2025; accepted 11 May 2026; published online 26 May 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s42003-026-10309-6 · PMID 42185520 · PMCID PMC13482815 · OpenAlex W7162317232
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism)
Methods: Connectivity, Statistics, Machine learning, fMRI & imaging, Single-unit activity, calcium imaging, Physiology & signal measures, Preprocessing
Keywords: Human behaviour, Gene expression, Network models
MeSH: Brain*, Imagination*, Transcriptome*, Visual Cortex*, Visual Perception*, Adult, Brain Mapping, Female, Gene Expression Profiling, Humans, Male, Young Adult (* major topic)
Topic: Face Recognition and Perception (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: National Natural Science Foundation of China (National Science Foundation of China) (32200840); STI2030-Major Projects (2021ZD0203803) the National Human Genetic Resources Sharing Service Platform (2005DKA21300)
Citations: not cited yet (Europe PMC); 70 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

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

figshare 31445032

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Statistics and Machine Learning Toolbox (2 files), Tools for NIfTI and ANALYZE image (MATLAB) (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
2 files
At the source:

Code availability statement

The paper has a code availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • it points to the authors' code: figshare 31445032

Read it in the paper: doi.org/10.1038/s42003-026-10309-6.

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;
  • 2 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 availability statement

The paper has a data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • no repository, dataset or request procedure was recognized in it

Read it in the paper: doi.org/10.1038/s42003-026-10309-6.

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 3 keywords, 12 MeSH terms, 2 funders, 67 references.

Cite

This paper

Xu, R., Zhang, D., Zhou, K., & Zhou, L. (2026). Predicting visual mental imagery: structural and transcriptomic signatures in the human brain. Communications biology, 9(1), 1113. https://doi.org/10.1038/s42003-026-10309-6

BibTeX

@article{xu2026predicting,
author = {Xu, Ruxin and Zhang, Dai and Zhou, Ke and Zhou, Liqin},
title = {{Predicting visual mental imagery: structural and transcriptomic signatures in the human brain}},
journal = {Communications biology},
year = {2026},
month = may,
volume = {9},
number = {1},
pages = {1113},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/s42003-026-10309-6},
url = {https://doi.org/10.1038/s42003-026-10309-6},
pmid = {42185520},
pmcid = {PMC13482815}
}

RIS

TY - JOUR
AU - Xu, Ruxin
AU - Zhang, Dai
AU - Zhou, Ke
AU - Zhou, Liqin
TI - Predicting visual mental imagery: structural and transcriptomic signatures in the human brain
T2 - Communications biology
J2 - Commun Biol
PY - 2026
DA - 2026/05/26
VL - 9
IS - 1
SP - 1113
SN - 2399-3642
PB - Nature Publishing Group
DO - 10.1038/s42003-026-10309-6
UR - https://doi.org/10.1038/s42003-026-10309-6
LA - en
ER -

CSL-JSON

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"id": "10.1038/s42003-026-10309-6",
"type": "article-journal",
"title": "Predicting visual mental imagery: structural and transcriptomic signatures in the human brain",
"container-title": "Communications biology",
"author": [
{
"family": "Xu",
"given": "Ruxin"
},
{
"family": "Zhang",
"given": "Dai"
},
{
"family": "Zhou",
"given": "Ke"
},
{
"family": "Zhou",
"given": "Liqin"
}
],
"container-title-short": "Commun Biol",
"volume": "9",
"issue": "1",
"page": "1113",
"DOI": "10.1038/s42003-026-10309-6",
"PMID": "42185520",
"PMCID": "PMC13482815",
"ISSN": "2399-3642",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s42003-026-10309-6",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
26
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]
}
}

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