The cross-site reproducibility of MRI morphometric phenotypes in psychiatric disorders.
The 6 matches · 4 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
- [1] § Methods › Quantifying the effects of sample and MRI data characteristics ↔ SBM/analysis/step10_covariates/step10k_corr_zmap_covariate_combine.m, the whole file · a weak match · score 0.78 · female ratio, illness duration, scanner model, control ratio, onset, voxel
- [2] § Methods › Quantifying the effects of sample and MRI data characteristics ↔ VBM/analysis/step10_figures/figure_covariates.m, the whole file · a weak match · score 0.76 · illness duration, scanner model, control ratio, properties, female, onset
- [3] § Methods › Measuring gray matter differences › SBM › Quality control procedures ↔ SBM/preprocessing/step2_autoQC/step2d_sub.mriqc_PCA.py, lines 138–148 · score 0.64 · Image quality, principal component, PCA, score, MRIQC, outliers
- [4] § Methods › Measuring gray matter differences › VBM › Quality control procedures ↔ VBM/preprocessing/step1_CAT12/CAT12_preprocessing_job.m, the whole file · a weak match · score 0.60 · CAT12 preprocessing, native, SPM12, MNI, VBM
- [5] § Methods › Measuring gray matter differences › SBM › Statistical analysis ↔ SBM/analysis/step6_statistical_analysis/step6_sub_make_input_run_mri_glmfit.sh, lines 57–122 · score 0.54 · mri_glmfit, Thresholded maps, FreeSurfer, permutation, ComBat
- [6] § Methods › Measuring gray matter differences › VBM › Region-level analyses ↔ VBM/analysis/step7_parcellation/step7b_sub_combine_parcellation.m, the whole file · a weak match · score 0.53 · Buckner cerebellar, subcortical, network, parcellated, Schaefer
Paper
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The authors' code
MATLAB · 126 lines · 4.9 KB · no license · 1 match
- function step10k_corr_zmap_covariate_combine(config)
- % STEP10K: Stack confound_*.mat from step10a-j into confound_combine.mat for figures.
- % Usage: step10k_corr_zmap_covariate_combine('config_hpc.json')
- % Prereq: run step10a through step10j first.
- % --- Load config and set paths ---
- if nargin < 1 || isempty(config)
- config = 'config_hpc.json';
- end
- this_dir = fileparts(mfilename('fullpath'));
- repo_root = fullfile(this_dir, '..', '..', '..');
- addpath(this_dir);
- addpath(genpath(fullfile(repo_root, 'utils')));
- if ischar(config) || isstring(config)
- config = pipeline_load_config(char(config));
- end
- % --- Paths from config ---
- data_root = config.data_directories.dataset_root;
- output_dir = fullfile(data_root, 'results', 'SBM', 'analysis', 'output');
- if ~exist(output_dir, 'dir'); mkdir(output_dir); end
- diagnosisString = {'BD', 'SCA', 'SCZ', 'ASD', 'MDD', 'AD'};
- conName = {'mean age','var age','male','female','sex ratio','patients','controls','subjects','patient HC ratio','treatment','mean EN','var EN','mean age onset','var age onset','mean illness duration','var illness duration','scanner brand','scanner model','voxel volume'};
- nCon = length(conName);
- nDiag = length(diagnosisString);
- % --- Load confound_*.mat and build combined tables ---
- % contoplot = table;
- for iDiag = 1:nDiag
- iCon = 0;
- iSite = 1;
- load(fullfile(output_dir, 'confound_age.mat'), 'varTable','meanAge', 'stdAge','nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1:iCon+2) = varTable{iDiag}{1,:};
- ptoplot(iDiag,iCon+1:iCon+2) = varTable{iDiag}{2,:};
- nSiteToPlot(iDiag,iCon+1:iCon+2) = nSite{iDiag}*ones(1,2);
- end
- iCon = iCon+2;
- iSite = iSite+1;
- load(fullfile(output_dir, 'confound_sex.mat'), 'varTable', 'maleRatio', 'femaleRatio', 'subjectRatio', 'maleFemaleRatio','nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1:iCon+3) = varTable{iDiag}{1,[1,2,4]};
- ptoplot(iDiag,iCon+1:iCon+3) = varTable{iDiag}{2,[1,2,4]};
- nSiteToPlot(iDiag,iCon+1:iCon+3) = nSite{iDiag}*ones(1,3);
- end
- iCon = iCon+3;
- iSite = iSite+1;
- load(fullfile(output_dir, 'confound_nPC.mat'), 'varTable','patientRatio', 'controlRatio', 'subjectRatio', 'patientControlRatio','nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1:iCon+4) = varTable{iDiag}{1,:};
- ptoplot(iDiag,iCon+1:iCon+4) = varTable{iDiag}{2,:};
- nSiteToPlot(iDiag,iCon+1:iCon+4) = nSite{iDiag}*ones(1,4);
- end
- iCon = iCon+4;
- iSite = iSite+1;
- load(fullfile(output_dir, 'confound_treatment.mat'), 'varTable','medRatio', 'nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1) = varTable{iDiag}{1,:};
- ptoplot(iDiag,iCon+1) = varTable{iDiag}{2,:};
- nSiteToPlot(iDiag,iCon+1) = nSite{iDiag};
- end
- iCon = iCon+1;
- iSite = iSite+1;
- load(fullfile(output_dir, 'confound_EN.mat'), 'varTable','meanEN','varEN','nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1:iCon+2) = varTable{iDiag}{1,:};
- ptoplot(iDiag,iCon+1:iCon+2) = varTable{iDiag}{2,:};
- nSiteToPlot(iDiag,iCon+1:iCon+2) = nSite{iDiag}*ones(1,2);
- end
- iCon = iCon+2;
- iSite = iSite+1;
- load(fullfile(output_dir, 'confound_ageonset.mat'), 'varTable', 'meanAgeOnset', 'stdAgeOnset','nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1:iCon+2) = varTable{iDiag}{1,:};
- ptoplot(iDiag,iCon+1:iCon+2) = varTable{iDiag}{2,:};
- nSiteToPlot(iDiag,iCon+1:iCon+2) = nSite{iDiag}*ones(1,2);
- end
- iCon = iCon+2;
- iSite = iSite+1;
- load(fullfile(output_dir, 'confound_illnessDuration.mat'), 'varTable','meanIllness', 'varIllness','nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1:iCon+2) = varTable{iDiag}{1,:};
- ptoplot(iDiag,iCon+1:iCon+2) = varTable{iDiag}{2,:};
- nSiteToPlot(iDiag,iCon+1:iCon+2) = nSite{iDiag}*ones(1,2);
- end
- iCon = iCon+2;
- iSite = iSite+1;
- load(fullfile(output_dir, 'confound_scanner.mat'), 'varTable','scannerSim','nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1) = varTable{iDiag}{1,:};
- ptoplot(iDiag,iCon+1) = varTable{iDiag}{2,:};
- nSiteToPlot(iDiag,iCon+1) = nSite{iDiag};
- end
- iCon = iCon+1;
- iSite = iSite+1;
- load(fullfile(output_dir, 'confound_scannerModel.mat'), 'varTable','modelSim','nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1) = varTable{iDiag}{1,:};
- ptoplot(iDiag,iCon+1) = varTable{iDiag}{2,:};
- nSiteToPlot(iDiag,iCon+1) = nSite{iDiag};
- end
- iCon = iCon+1;
- iSite = iSite+1;
- load(fullfile(output_dir, 'confound_vol.mat'), 'varTable','volRatio','nSite');
- if ~isempty(varTable{iDiag})
- contoplot(iDiag,iCon+1) = varTable{iDiag}{1,:};
- ptoplot(iDiag,iCon+1) = varTable{iDiag}{2,:};
- nSiteToPlot(iDiag,iCon+1) = nSite{iDiag};
- end
- pvals_bonf(iDiag,:) = min(ptoplot(iDiag,:).* size(ptoplot,2), 1);
- end
- % --- Save confound_combine.mat ---
- save(fullfile(output_dir, 'confound_combine.mat'),'ptoplot','pvals_bonf','contoplot','nSiteToPlot');
- end
step10k_corr_zmap_covariate_combine.m at commit 2260406, no license · at the source
Overview
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, Clayton, Victoria Australia
- Department of Neuroscience, Yale School of Medicine, New Haven, CT USA
- Wu Tsai Institute, Yale University, New Haven, CT USA
- Centre for Integrative Neuroimaging (OxCIN), FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Orygen, The National Centre of Excellence in Youth Mental Health, Parkville, Victoria Australia
- Centre for Youth Mental Health, The University of Melbourne, Parkville, Victoria Australia
- Centre for Sleep and Cognition & Centre for Translational Magnetic Resonance Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Electrical and Computer Engineering & Integrative Sciences and Engineering Programme (ISEP), NUS Graduate School, National University of Singapore, Singapore, Singapore
- Memory Aging and Cognition Centre, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Psychiatry, The University of Melbourne, Parkville, Victoria Australia
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, with 6 matches between paragraphs and lines of code.
NSBLab/reproducibility_grey_matter_differences_in_disorders
2260406ee295042a6cdb51cb147400e07007f2f6, 2 August 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
343 files
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preprocessing/ , MATLAB, 182 linesstep4_extract_subjects/ extract_sub_surface_Myel in.m - SBM/
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preprocessing/ , Python, 39 linesstep5_combat/ COMBAT_surface_run.py - SBM/
preprocessing/ , MATLAB, 157 linesstep5_combat/ step5a_combine_metadata. m - SBM/
preprocessing/ , Shell, 38 linesstep5_combat/ step5b_combat_surface_in put.sh - SBM/
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preprocessing/ , Shell, 25 linesstep4_combat/ step4e_sub_combat_output .sh - data_BIDS/
BIDS_Myelin.m , MATLAB, 170 lines - data_BIDS/
BIDS_RD.m , MATLAB, 115 lines - data_BIDS/
extract_file.sh , Shell, 6 lines - data_BIDS/
extract_med.m , MATLAB, 30 lines - data_BIDS/
if_med.m , MATLAB, 57 lines - data_BIDS/
if_onset.m , MATLAB, 20 lines - data_BIDS/
step0a_create_dataset_li , MATLAB, 36 linesst.m - data_BIDS/
step0b_organize_bids.m , MATLAB, 46 lines - utils/
MRIread.m , MATLAB, 287 lines - utils/
bin_corr_mat.m , MATLAB, 47 lines - utils/
bin_corr_mat_account_zer , MATLAB, 54 lineso.m - utils/
bluewhitered.m , MATLAB, 101 lines - utils/
bramila_mantel.m , MATLAB, 63 lines - utils/
drawbrace.m , MATLAB, 80 lines - utils/
execution_utils.py , Python, 171 lines - utils/
greenwhiteviolet.m , MATLAB, 101 lines - utils/
modes/ , MATLAB, 58 linescalc_eigendecomposition. m - utils/
modes/ , MATLAB, 84 linescalc_eigenreconstruction .m - utils/
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modes/ , MATLAB, 162 linescalc_mass_stiffness.m - utils/
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modes/ , MATLAB, 99 linescheckVertsFacesRoisData. m - utils/
modes/ , MATLAB, 15 linesgetAllEigengroupIdx.m - utils/
modes/ , MATLAB, 7 linesgetEigengroupIdx.m - utils/
modes/ , MATLAB, 123 linestriangulation2adjacency. m - utils/
modes/ , MATLAB, 171 linestrimExcludedRois.m - utils/
modes/ , MATLAB, 23 linesunmask.m - utils/
multipleAxes.m , MATLAB, 31 lines - utils/
pipeline_ensure_paths.m , MATLAB, 16 lines - utils/
pipeline_get_enabled_dat , MATLAB, 17 linesasets.m - utils/
pipeline_get_repo_root.m , MATLAB, 8 lines - utils/
pipeline_load_config.m , MATLAB, 17 lines - utils/
pipeline_resolve_config_ , MATLAB, 17 linesvariables.m - utils/
pipeline_resolve_relativ , MATLAB, 16 linese_path.m - utils/
plot_map.m , MATLAB, 25 lines - utils/
read_annotation.m , MATLAB, 130 lines - utils/
read_vtk.m , MATLAB, 90 lines - utils/
replication_mat.m , MATLAB, 30 lines - utils/
save_mgh.m , MATLAB, 102 lines - README.md, Text, 108 lines
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: NSBLab/
reproducibility_grey_mat ter_differences_in_disor ders
Read it in the paper: doi.org/10.1038/s41593-026-02359-0.
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;
- 342 scripts, each with its path and the digest of its content;
- 6 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 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/s41593-026-02359-0.
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, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 18 authors, 2 keywords, 10 MeSH terms, 7 funders, 107 references.
Cite
This paper
Cao, T., Pang, J. C., Gajwani, M., Segal, A., Holmes, A., Wiley, J. F., Chopra, S., Zhou, J. H., Chen, C. L. H., Ji, F., Harrison, B. J., Davey, C. G., Constable, T., Tiego, J., Hartshorn, B., Kwee, J., Bellgrove, M. A., & Fornito, A. (2026). The cross-site reproducibility of MRI morphometric phenotypes in psychiatric disorders. Nature neuroscience, 29(9), 2273-2282. https://
BibTeX
@article{cao2026cross,
author = {Cao, Trang and Pang, James C and Gajwani, Mehul and Segal, Ashlea and Holmes, Alexander and Wiley, Joshua F and Chopra, Sidhant and Zhou, Juan Helen and Chen, Christopher L H and Ji, Fang and Harrison, Ben J and Davey, Christopher G and Constable, Toby and Tiego, Jeggan and Hartshorn, Bree and Kwee, Jessica and Bellgrove, Mark A and Fornito, Alex},
title = {{The cross-site reproducibility of MRI morphometric phenotypes in psychiatric disorders}},
journal = {Nature neuroscience},
year = {2026},
month = jul,
volume = {29},
number = {9},
pages = {2273--2282},
publisher = {Nature Portfolio},
issn = {1097-6256},
doi = {10.1038/
url = {https://
pmid = {42533130},
pmcid = {PMC13533841}
}
RIS
TY - JOUR
AU - Cao, Trang
AU - Pang, James C
AU - Gajwani, Mehul
AU - Segal, Ashlea
AU - Holmes, Alexander
AU - Wiley, Joshua F
AU - Chopra, Sidhant
AU - Zhou, Juan Helen
AU - Chen, Christopher L H
AU - Ji, Fang
AU - Harrison, Ben J
AU - Davey, Christopher G
AU - Constable, Toby
AU - Tiego, Jeggan
AU - Hartshorn, Bree
AU - Kwee, Jessica
AU - Bellgrove, Mark A
AU - Fornito, Alex
TI - The cross-site reproducibility of MRI morphometric phenotypes in psychiatric disorders
T2 - Nature neuroscience
J2 - Nat Neurosci
PY - 2026
DA - 2026/
VL - 29
IS - 9
SP - 2273
EP - 2282
SN - 1097-6256
PB - Nature Portfolio
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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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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