The "Brain's Traffic Map" Reveals Neural Pathways Linked to Coronary Microvascular Dysfunction in Women.
Paper
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The authors' code
MATLAB · 287 lines · 12 KB · no license
- clear;
- clc;
- % Constants
- num_aal = 90; % replace with appropriate number of brain regions specific to the atlas image that is aimed to be used
- listpath = fullfile('path_to_lists_directory'); % Replace with appropriate path for the subject list
- datapath = fullfile('path_to_fc_matrices'); % Replace with appropriate path for FC matrices
- outputpath = fullfile('path_to_output_directory'); % Replace with appropriate path
- % SC = structural connectivity
- % FC = functional connectivity
- % Load necessary data as .mat file
- load('AAL_ind_116to90.mat'); % update index (ind): AAL atlas compressed to 90 investigated regions such removing cerebellum and vermis from the atlas
- % Import subject IDs with both FC and SC matrices
- subjects_both = importSubjIDs(fullfile(listpath, 'HCP_1200_list_both_fmask.txt')); %replace with appropriate file name for subject list
- num_s = length(subjects_both);
- % Load or compute center of mass and distance matrices
- outfile1 = 'CMs_AAL_adult_90AAL.mat'; %replace with the atlas specific indices
- if ~exist(outfile1, 'file')
- AAL_data = niftiread('AAL.nii'); % replace with appropriate atlas image that is aimed to be used
- ROIs = unique(AAL_data);
- ROIs(ROIs == 0) = []; % remove background
- CMs = zeros(length(ROIs), 3);
- for idx = 1:length(ROIs)
- [x, y, z] = ind2sub(size(AAL_data), find(AAL_data == ROIs(idx)));
- CMs(idx, :) = [mean(x), mean(y), mean(z)];
- end
- CM_90 = CMs(ind, :);
- save(outfile1, 'CMs', 'CM_90', 'ind');
- end
- outfile2 = 'Distance_CMs_AAL_adult_90AAL.mat';
- if ~exist(outfile2, 'file')
- load(outfile1);
- Distance_90 = zeros(num_aal, num_aal); %replace with appropriate number of brain regions for a specific atlas
- for rr = 1:num_aal
- for rrr = rr:num_aal
- Distance_90(rr, rrr) = norm(CM_90(rr, :) - CM_90(rrr, :));
- Distance_90(rrr, rr) = Distance_90(rr, rrr);
- end
- end
- save(outfile2, 'Distance_90');
- end
- % Main computation loop
- for ss = 1:num_s
- fprintf('Calculating for subject %d\n', ss);
- subj = subjects_both{ss};
- % Define file paths
- finfile = fullfile(outputpath, 'FC_Matrices_FDR_corrected_90AAL', [subj '_Functional_Matrix_FDR_corrected.mat']);%replace with appropriate file name for FC
- sinfile = fullfile(outputpath, 'Structural_Matrices_individual_nothr_90AAL', [subj '_Structural_Matrix.mat']); %%replace with appropriate file name for SC
- outputdir_USFC = fullfile('path_to_output_USFC_directory'); % Replace with appropriate path
- if ~exist(outputdir_USFC, 'dir')
- mkdir(outputdir_USFC);
- end
- % Check if output files already exist
- outfile_all = fullfile(outputdir_USFC, [subj '_Cost_Route_all_Matrix.mat']);
- if ~exist(outfile_all, 'file')
- load(finfile);
- load(sinfile);
- % Make the economical assumption to find the most efficient segments up to 4 steps
- Cost_M = Distance_90 ./ Structural_M;
- Min_cost_M = inf(num_aal, num_aal);
- Route_M = cell(num_aal, num_aal);
- for rr = 1:(num_aal - 1)
- for rrr = (rr + 1):num_aal
- if Functional_M(rr, rrr) ~= 0
- % Find minimum cost routes (up to 4 steps)
- min_routes = cell(4, 1);
- min_costs = zeros(4, 1);
- min_costs(1) = Cost_M(rr, rrr);
- min_routes{1} = [rr, rrr];
- % 2 steps
- [min_cost, I1] = min(Cost_M(rr, :) + Cost_M(:, rrr)');
- min_costs(2) = min_cost;
- min_routes{2} = [rr, I1, rrr];
- % 3 steps
- costs = arrayfun(@(x, y) Cost_M(rr, x) + Cost_M(x, y) + Cost_M(y, rrr), 1:num_aal, 1:num_aal);
- [min_cost, I] = min(costs(:));
- [I1, I2] = ind2sub(size(costs), I);
- min_costs(3) = min_cost;
- min_routes{3} = [rr, I1, I2, rrr];
- % 4 steps
- costs = arrayfun(@(x, y, z) Cost_M(rr, x) + Cost_M(x, y) + Cost_M(y, z) + Cost_M(z, rrr), 1:num_aal, 1:num_aal, 1:num_aal);
- [min_cost, I] = min(costs(:));
- [I1, I2, I3] = ind2sub(size(costs), I);
- min_costs(4) = min_cost;
- min_routes{4} = [rr, I1, I2, I3, rrr];
- % Select the minimum route
- [All_min_cost, All_I] = min(min_costs);
- Min_cost_M(rr, rrr) = All_min_cost;
- if ~isinf(All_min_cost)
- Route_M{rr, rrr} = min_routes{All_I};
- end
- end
- end
- end
- % Symmetrize matrices
- It = logical(tril(ones(num_aal, num_aal), -1));
- Min_cost_M(It) = Min_cost_M';
- Route_M(It) = Route_M';
- % Save the results
- save(outfile_all, 'Cost_M', 'Min_cost_M', 'Route_M');
- end
- % Route-specific matrices
- Route_M1_eff = cell(num_aal, num_aal);
- Route_M2_eff = cell(num_aal, num_aal);
- Route_M3_eff = cell(num_aal, num_aal);
- Route_M4_eff = cell(num_aal, num_aal);
- for rr = 1:(num_aal-1)
- for rrr = rr+1:num_aal
- route_len = length(Route_M{rr, rrr});
- switch route_len
- case 2
- Route_M1_eff{rr, rrr} = Route_M{rr, rrr};
- case 3
- Route_M2_eff{rr, rrr} = Route_M{rr, rrr};
- case 4
- Route_M3_eff{rr, rrr} = Route_M{rr, rrr};
- case 5
- Route_M4_eff{rr, rrr} = Route_M{rr, rrr};
- end
- end
- end
- % Symmetrize the route matrices
- It = logical(tril(ones(num_aal,num_aal),-1));
- Route_M1_eff(It) = Route_M1_eff';
- Route_M2_eff(It) = Route_M2_eff';
- Route_M3_eff(It) = Route_M3_eff';
- Route_M4_eff(It) = Route_M4_eff';
- % Save route-specific matrices
- save(fullfile(outputdir_USFC, [subj '_Route1_Matrix.mat']), 'Route_M1_eff');
- save(fullfile(outputdir_USFC, [subj '_Route2_Matrix.mat']), 'Route_M2_eff');
- save(fullfile(outputdir_USFC, [subj '_Route3_Matrix.mat']), 'Route_M3_eff');
- save(fullfile(outputdir_USFC, [subj '_Route4_Matrix.mat']), 'Route_M4_eff');
- % Further processing and saving FC and SC matrices
- outfile_FC_M1 = fullfile(outputdir_USFC, [subj '_FC_R1_Matrix.mat']);
- outfile_FC_M2 = fullfile(outputdir_USFC, [subj '_FC_R2_Matrix.mat']);
- outfile_FC_M3 = fullfile(outputdir_USFC, [subj '_FC_R3_Matrix.mat']);
- outfile_FC_M4 = fullfile(outputdir_USFC, [subj '_FC_R4_Matrix.mat']);
- outfile_USFC_all = fullfile(outputdir_USFC, [subj '_USFC_Matrix.mat']);
- outfile_USFC_all_abs = fullfile(outputdir_USFC, [subj '_USFC_Matrix_abs.mat']);
- outfile_Route_count = fullfile(outputdir_USFC, [subj '_USFC_Route_count_Matrix.mat']);
- if ~exist(outfile_FC_M1, 'file')
- load(finfile);
- load(sinfile);
- SC_M1 = zeros(num_aal, num_aal);
- SC_M2 = zeros(num_aal, num_aal);
- SC_M3 = zeros(num_aal, num_aal);
- SC_M4 = zeros(num_aal, num_aal);
- FC_M1 = zeros(num_aal, num_aal);
- FC_M2 = zeros(num_aal, num_aal);
- FC_M3 = zeros(num_aal, num_aal);
- FC_M4 = zeros(num_aal, num_aal);
- % Construct the SC and FC for each step
- for rr = 1:num_aal
- for rrr = 1:num_aal
- Route = Route_M{rr, rrr};
- if ~isempty(Route)
- n_steps = length(Route);
- switch n_steps
- case 2
- SC_M1(rr, rrr) = Structural_M(Route(1), Route(2));
- FC_M1(rr, rrr) = Functional_M(Route(1), Route(2));
- case 3
- SC_M2(rr, rrr) = (Structural_M(Route(1), Route(2)) + Structural_M(Route(2), Route(3))) / 2;
- FC_M2(rr, rrr) = Functional_M(Route(1), Route(3));
- case 4
- SC_M3(rr, rrr) = (Structural_M(Route(1), Route(2)) + Structural_M(Route(2), Route(3)) + Structural_M(Route(3), Route(4))) / 3;
- FC_M3(rr, rrr) = Functional_M(Route(1), Route(4));
- case 5
- SC_M4(rr, rrr) = (Structural_M(Route(1), Route(2)) + Structural_M(Route(2), Route(3)) + Structural_M(Route(3), Route(4)) + Structural_M(Route(4), Route(5))) / 4;
- FC_M4(rr, rrr) = Functional_M(Route(1), Route(5));
- end
- end
- end
- end
- % Symmetrize matrices
- SC_M1(It) = SC_M1';
- SC_M2(It) = SC_M2';
- SC_M3(It) = SC_M3';
- SC_M4(It) = SC_M4';
- FC_M1(It) = FC_M1';
- FC_M2(It) = FC_M2';
- FC_M3(It) = FC_M3';
- FC_M4(It) = FC_M4';
- % Save the results
- save(outfile_FC_M1, 'FC_M1');
- save(outfile_FC_M2, 'FC_M2');
- save(outfile_FC_M3, 'FC_M3');
- save(outfile_FC_M4, 'FC_M4');
- end
- % Calculate and save USFC matrices
- if ~exist(outfile_USFC_all, 'file')
- USFC_M = zeros(num_aal, num_aal);
- USFC_M_abs = zeros(num_aal, num_aal);
- RouteCounts_M = zeros(num_aal, num_aal);
- for rr = 1:num_aal
- for rrr = 1:num_aal
- Route = Route_M{rr, rrr};
- if ~isempty(Route)
- n_steps = length(Route) - 1;
- for nn = 1:n_steps
- step_i = Route(nn);
- step_j = Route(nn+1);
- if step_i < step_j
- USFC_M(step_i, step_j) = USFC_M(step_i, step_j) + Functional_M(rr, rrr);
- USFC_M_abs(step_i, step_j) = USFC_M_abs(step_i, step_j) + abs(Functional_M(rr, rrr));
- RouteCounts_M(step_i, step_j) = RouteCounts_M(step_i, step_j) + 1;
- elseif step_j < step_i
- USFC_M(step_j, step_i) = USFC_M(step_j, step_i) + Functional_M(rrr, rr);
- USFC_M_abs(step_j, step_i) = USFC_M_abs(step_j, step_i) + abs(Functional_M(rrr, rr));
- RouteCounts_M(step_j, step_i) = RouteCounts_M(step_j, step_i) + 1;
- end
- end
- end
- end
- end
- % Symmetrize matrices
- USFC_M(It) = USFC_M';
- USFC_M_abs(It) = USFC_M_abs';
- RouteCounts_M(It) = RouteCounts_M';
- % Save the results
- save(outfile_USFC_all, 'USFC_M');
- save(outfile_USFC_all_abs, 'USFC_M_abs');
- save(outfile_Route_count, 'RouteCounts_M');
- end
- % Save the SC and FC matrices as edge files for further analysis and plotting (replace with appropriate paths)
- baseFolder_SC_M = fullfile('path_to_SC_M_directory');
- if ~exist(baseFolder_SC_M, 'dir')
- mkdir(baseFolder_SC_M);
- end
- saveAsEdge(SC_M1, fullfile(baseFolder_SC_M, [subj, '_SC_M1.edge']));
- saveAsEdge(SC_M2, fullfile(baseFolder_SC_M, [subj, '_SC_M2.edge']));
- saveAsEdge(SC_M3, fullfile(baseFolder_SC_M, [subj, '_SC_M3.edge']));
- saveAsEdge(SC_M4, fullfile(baseFolder_SC_M, [subj, '_SC_M4.edge']));
- baseFolder_FC_M = fullfile('path_to_FC_M_directory');
- if ~exist(baseFolder_FC_M, 'dir')
- mkdir(baseFolder_FC_M);
- end
- saveAsEdge(FC_M1, fullfile(baseFolder_FC_M, [subj, '_FC_M1.edge']));
- saveAsEdge(FC_M2, fullfile(baseFolder_FC_M, [subj, '_FC_M2.edge']));
- saveAsEdge(FC_M3, fullfile(baseFolder_FC_M, [subj, '_FC_M3.edge']));
- saveAsEdge(FC_M4, fullfile(baseFolder_FC_M, [subj, '_FC_M4.edge']));
- baseFolder_USFC_M = fullfile('path_to_USFC_M_directory');
- if ~exist(baseFolder_USFC_M, 'dir')
- mkdir(baseFolder_USFC_M);
- end
- saveAsEdge(USFC_M, fullfile(baseFolder_USFC_M, [subj, '_USFC.edge']));
- saveAsEdge(USFC_M_abs, fullfile(baseFolder_USFC_M, [subj, '_USFC_abs.edge']));
- baseFolder_Route = fullfile('path_to_Route_directory');
- if ~exist(baseFolder_Route, 'dir')
- mkdir(baseFolder_Route);
- end
- saveAsEdge(RouteCounts_M, fullfile(baseFolder_Route, [subj, '_Route_counted.edge']));
- end
USFC.m at commit b39b850, no license · at the source
Overview
- Department of Neurology, Cedars‐Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences and Imaging, Biomedical Imaging Research Institute (BIRI), Cedars‐Sinai Medical Center, Los Angeles, California, USA
- Department of Physical Medicine and Rehabilitation, Cedars‐Sinai Medical Center, Los Angeles, California, USA
- Barbra Streisand Women's Heart Center, Smidt Heart Institute, Cedars‐Sinai Medical Center, Los Angeles, California, USA
- Department of Neurology, Mayo Clinic College of Medicine and Science, Scottsdale, Arizona, USA
- Departments of Neurology and Medicine, Cedars‐Sinai Medical Center, Los Angeles, California, USA
- Department of Kinesiology, College of Nursing and Health Innovation, The University of Texas at Arlington, Arlington, Texas, USA
Abstract
Background: The brain–heart axis is central to vascular health, yet no imaging biomarkers capture integrated dysfunction across neural and coronary microvascular networks. Although coronary microvascular dysfunction links to cognitive decline, neural correlates connecting cerebral efficiency with coronary physiology remain unclear.
Objectives: To determine whether the Unified Structural and Functional Connectivity (USFC)—a multimodal magnetic resonance imaging (MRI) “traffic map” of brain network efficiency—predicts coronary endothelial function and cognition in women with ischemia and no obstructive coronary artery disease (INOCA).
Methods: Thirty‐three women with suspected INOCA from the Women's Ischemia Syndrome Evaluation (WISE) study (NCT03876223) underwent invasive coronary function testing, cardiac MRI, cognitive evaluation, and multimodal brain MRI. USFC, structural connectivity (SC), and functional connectivity (FC) were computed for predefined 10 backbone pathways. Support vector regression and logistic classification assessed predictive performance.
Results: USFC explained 16%–20% more variance in coronary endothelial function, myocardial perfusion reserve, and cognition than SC or FC alone (p < 0.05). Connectivity between the left caudate–superior medial orbital gyrus and right calcarine–inferior occipital gyrus emerged as robust predictors of crystallized cognition (r = –0.78, p FDR < 0.05) and coronary endothelial function (r = 0.70, p FDR < 0.05), respectively. USFC also best discriminated low versus high coronary blood flow (area under the ROC curve [AUC]: USFC 0.622 vs. SC 0.349 and FC 0.425; p < 0.05).
Conclusions: USFC identifies neuro–cardiac pathways linking cerebral efficiency with coronary endothelial function. These results introduce a sensitive biomarker of systemic vulnerability, highlighting occipital and frontostriatal pathways as shared substrates of dysfunction. USFC offers a mechanistic framework for detecting vascular risk across metabolically demanding tissues.
Trial Registration: ClinicalTrials.gov identifier: NCT03876223
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above.
ArzuHas/USFC
b39b8501beb2b42bb7930556a5286e8be3c27a64, 10 October 2024Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
4 files
- USFC.m, MATLAB, 287 lines
- importSubjIDs.m, MATLAB, 48 lines
- saveAsEdge.m, MATLAB, 16 lines
- README.md, Text, 78 lines
Zenodo 13997197
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
- 27 September 2026: the link answers (HTTP 200)
4 files
- USFC.m, MATLAB, 287 lines
- importSubjIDs.m, MATLAB, 48 lines
- saveAsEdge.m, MATLAB, 16 lines
- README.md, Text, 78 lines
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:
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- no match between paragraphs and code yet;
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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 datasets used and/
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, 13 authors, 6 keywords, 10 MeSH terms, 13 funders, 46 references.
Cite
This paper
Has Silemek, A. C., Wertheimer, J. C., Wei, J., Xie, Y., Gonzales, M., Li, D., Dumitrascu, O., Kremen, S., Tan, Z. S., Nelson, M. D., Bairey Merz, C. N., Sati, P., & Gao, W. (2026). The "Brain's Traffic Map" Reveals Neural Pathways Linked to Coronary Microvascular Dysfunction in Women. Brain and behavior, 16(6), e71559. https://
BibTeX
@article{hassilemek2026b
author = {Has Silemek, Arzu C and Wertheimer, Jeffrey C and Wei, Janet and Xie, Yibin and Gonzales, Mitzi and Li, Debiao and Dumitrascu, Oana and Kremen, Sarah and Tan, Zaldy S and Nelson, Micheal D and Bairey Merz, C Noel and Sati, Pascal and Gao, Wei},
title = {{The "Brain's Traffic Map" Reveals Neural Pathways Linked to Coronary Microvascular Dysfunction in Women}},
journal = {Brain and behavior},
year = {2026},
month = jun,
volume = {16},
number = {6},
pages = {e71559},
publisher = {Wiley},
issn = {2162-3279},
doi = {10.1002/
url = {https://
pmid = {42348298},
pmcid = {PMC13296822}
}
RIS
TY - JOUR
AU - Has Silemek, Arzu C
AU - Wertheimer, Jeffrey C
AU - Wei, Janet
AU - Xie, Yibin
AU - Gonzales, Mitzi
AU - Li, Debiao
AU - Dumitrascu, Oana
AU - Kremen, Sarah
AU - Tan, Zaldy S
AU - Nelson, Micheal D
AU - Bairey Merz, C Noel
AU - Sati, Pascal
AU - Gao, Wei
TI - The "Brain's Traffic Map" Reveals Neural Pathways Linked to Coronary Microvascular Dysfunction in Women
T2 - Brain and behavior
J2 - Brain Behav
PY - 2026
DA - 2026/
VL - 16
IS - 6
SP - e71559
SN - 2162-3279
PB - Wiley
DO - 10.1002/
UR - https://
LA - en
ER -
CSL-JSON
{
"id": "10.1002/
"type": "article-journal",
"title": "The \"Brain's Traffic Map\" Reveals Neural Pathways Linked to Coronary Microvascular Dysfunction in Women",
"container-title": "Brain and behavior",
"author": [
{
"family": "Has Silemek",
"given": "Arzu C"
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"given": "Jeffrey C"
},
{
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"given": "Yibin"
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{
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"given": "Mitzi"
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{
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"given": "Debiao"
},
{
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"given": "Oana"
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{
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"given": "Sarah"
},
{
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"given": "Zaldy S"
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{
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{
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"given": "Pascal"
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}
],
"container-title-short":
"volume": "16",
"issue": "6",
"page": "e71559",
"DOI": "10.1002/
"PMID": "42348298",
"PMCID": "PMC13296822",
"ISSN": "2162-3279",
"publisher": "Wiley",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
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1
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]
}
}
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Validate its tracing map
You validate the map as this page shows it: 2 repositories of the authors' code, each at its verified commit and with its license, 6 scripts, and 0 matches between paragraphs and code (see the Code and Map sections). It then receives a DOI on Zenodo, with you (your ORCID iD) and OSCR as its creators; the code itself is not deposited.
The map's fingerprint: sha256:62d3152e4a6b3c13…
Add the badge to its README
The badge links the code to this page. Copy one of these into the README of the paper's code: only you decide where it goes, and nothing is changed for you.
Markdown
[, paste the snippet at the top, then “Commit changes…” and, to review it first, “Create a new branch and start a pull request”. You open the pull request; OSCR asks for no permission.
Request its removal
To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).
Discussion, reproductions, activity
Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.
Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.
Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.
