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Higher-order functional connectivity and topological analysis of multichannel fNIRS data.

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Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Jupyter notebook · 33 lines · 752 B · no license

  1. # %%
  3. import numpy as np
  4. import scipy.io as sio
  5. from scipy.stats import zscore
  8. def compute_fc(ts, do_zscore=True):
  9. """
  10. ts: (N, T) channels x time
  11. returns: (N, N) FC correlation matrix
  12. """
  13. ts = np.asarray(ts, dtype=float)
  14. if do_zscore:
  15. ts = zscore(ts, axis=1, nan_policy="omit")
  16. return np.corrcoef(ts)
  18. def compute_eFC(ts, do_zscore=True):
  19. """
  20. Edge functional connectivity from time series.
  21. ts: (N, T)
  22. returns: (E, E) where E = N*(N-1)/2
  23. """
  24. ts = np.asarray(ts, dtype=float)
  25. if do_zscore:
  26. ts = zscore(ts, axis=1, nan_policy="omit")
  28. N, T = ts.shape
  29. u, v = np.triu_indices(N, k=1)
  30. edge_ts = ts[u, :] * ts[v, :]
  31. return np.corrcoef(edge_ts)

fc.ipynb at commit e15793d, no license · at the source

Overview

Authors: Hailing Luo1, Yuejia Luo1,2,3, Lian Duan1,2,3
  1. School of Psychology, Shenzhen University, Shenzhen, China
  2. Shenzhen Key Laboratory of Affective and Social Neuroscience, Center for Brain Disorders and Cognitive Sciences, Shenzhen University, Shenzhen, China
  3. Key Laboratory of Brain Cognition and Emotional Health of Guangdong Higher Education Institutes, Shenzhen University, Shenzhen, China
Institutions: Shenzhen University (China)
Journal: Biomedical optics express, volume 17, issue 5, pages 2626-2642
Dates: received 6 January 2026; accepted 13 April 2026; published online 24 April 2026
Type: Research article · Language: English
License: none stated
Identifiers: DOI 10.1364/boe.589685 · PMID 42145691 · PMCID PMC13178594 · OpenAlex W7154631035
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: fNIRS (modality)
Methods: Spectral & time-frequency, Connectivity, Statistics, Smoothing, state filtering, decompositions, Preprocessing
Topic: Topological and Geometric Data Analysis (Computational Theory and Mathematics, Computer Science), according to OpenAlex
Funding: Shenzhen Science and Technology Innovation Program (JCYJ20210324093208021); Shenzhen-Hong Kong Institute of Brain Science (2023SHIBS0004)
Citations: not cited yet (Europe PMC); 33 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (none stated) 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.

hailing613/fnirs_fc

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: e15793d7fc880f33ee2114c568dd53b0eccd9ebf, 27 March 2026
Languages: Jupyter (1)
Size: 2 files, 1 script
Software Heritage: not archived
Found in: the text, “Edge-level Functional Connectivity (eFC).”
Holds: README, 1 notebook
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: NumPy (1 file), SciPy (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
2 files
At the source: github.com/hailing613/fnirs_fc.git

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

No dataset and no data link were found in the paper.

Data availability statement

The paper has a data availability statement. Its license (none stated) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • it says that the data are available on request

Read it in the paper: doi.org/10.1364/boe.589685.

Versions

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Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 2 funders, 33 references.

Cite

This paper

Luo, H., Luo, Y., & Duan, L. (2026). Higher-order functional connectivity and topological analysis of multichannel fNIRS data. Biomedical optics express, 17(5), 2626-2642. https://doi.org/10.1364/boe.589685

BibTeX

@article{luo2026higher,
author = {Luo, Hailing and Luo, Yuejia and Duan, Lian},
title = {{Higher-order functional connectivity and topological analysis of multichannel fNIRS data}},
journal = {Biomedical optics express},
year = {2026},
month = apr,
volume = {17},
number = {5},
pages = {2626--2642},
publisher = {Optica Publishing Group},
issn = {2156-7085},
doi = {10.1364/boe.589685},
url = {https://doi.org/10.1364/boe.589685},
pmid = {42145691},
pmcid = {PMC13178594}
}

RIS

TY - JOUR
AU - Luo, Hailing
AU - Luo, Yuejia
AU - Duan, Lian
TI - Higher-order functional connectivity and topological analysis of multichannel fNIRS data
T2 - Biomedical optics express
J2 - Biomed Opt Express
PY - 2026
DA - 2026/04/24
VL - 17
IS - 5
SP - 2626
EP - 2642
SN - 2156-7085
PB - Optica Publishing Group
DO - 10.1364/boe.589685
UR - https://doi.org/10.1364/boe.589685
LA - en
ER -

CSL-JSON

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"id": "10.1364/boe.589685",
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"title": "Higher-order functional connectivity and topological analysis of multichannel fNIRS data",
"container-title": "Biomedical optics express",
"author": [
{
"family": "Luo",
"given": "Hailing"
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{
"family": "Luo",
"given": "Yuejia"
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{
"family": "Duan",
"given": "Lian"
}
],
"container-title-short": "Biomed Opt Express",
"volume": "17",
"issue": "5",
"page": "2626-2642",
"DOI": "10.1364/boe.589685",
"PMID": "42145691",
"PMCID": "PMC13178594",
"ISSN": "2156-7085",
"publisher": "Optica Publishing Group",
"URL": "https://doi.org/10.1364/boe.589685",
"language": "en",
"issued": {
"date-parts": [
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2026,
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}
}

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