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Examining neuroimaging biomarkers, plasma biomarkers and cognitive functions in patients with recovered COVID-19 infection: a multicentre study using 7T MRI.

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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

Python · 31 lines · 794 B · no license

  1. from setuptools import setup, find_packages
  3. setup(
  4. name='wmh_seg',
  5. version='1.6.0',
  6. packages=find_packages(),
  7. include_package_data=True,
  8. package_data={'wmh_seg': ['nnunet_assets/*/*.json']},
  9. description='WMH segmentation for FLAIR images',
  10. author='Jinghang Li',
  11. author_email='[email hidden]',
  12. url='https://github.com/jinghangli98/wmh_seg', # Replace with your GitHub repo
  13. install_requires=[
  14. 'tqdm',
  15. 'torch',
  16. 'torchvision',
  17. 'nibabel',
  18. 'einops',
  19. 'torchio',
  20. "timm==0.6.12",
  21. 'numpy',
  22. 'segmentation-models-pytorch==0.3.2',
  23. 'huggingface_hub',
  24. 'nnunetv2',
  25. ],
  26. entry_points={
  27. 'console_scripts': [
  28. 'wmh_seg=wmh_seg.cli:main',
  29. ],
  30. },
  31. )

setup.py at commit a5ad55c, no license · at the source

Overview

Authors: Jr-Jiun Liou1, Tales Santini1, Jinghang Li1, Monica Gireud-Goss2, Tiffany F Kautz2, Julie Parker-Garza2, Juan Carlos Guerrero2, Vibhuti Patel2, Oluwatobi F Adeyemi3, Gabriel A de Erausquin2, Valentina R Garbarino2, Mohamad Habes2, Jayandra J Himali2, Christof Karmonik4, Beth E Snitz1, Joseph M Mettenburg1, Minjie Wu1, Howard J Aizenstein1, Anna L Marsland1, Peter J Gianaros1
and 11 other authorsRichard Bowtell3, Olivier Mougin3, Penny A Gowland3, Mohammad Zia Katshu3, Farhaan S Vahidy4, Timothy D Girard1, Heidi I L Jacobs5, Akram A Hosseini3, Sudha Seshadri2, Tamer S Ibrahim1, 7T MRI COVID Consortium
ORCID iDs: Jr-Jiun Liou, Tales Santini, Mohamad Habes, Peter J Gianaros, Penny A Gowland, Heidi I L Jacobs
  1. University of Pittsburgh, Pittsburgh, PA 15260, USA
  2. University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
  3. University of Nottingham, Nottingham NG7 2RD, UK
  4. Houston Methodist Research Institute, Houston, TX 77030, USA
  5. Massachusetts General Hospital, Harvard University, Boston, MA 02114, USA
Institutions: University of Pittsburgh (United States); The University of Texas at San Antonio Health Science Center (United States); University of Nottingham (United Kingdom); Houston Methodist (United States); Harvard University (United States); Massachusetts General Hospital (United States)
Journal: Brain communications, volume 8, issue 2, article fcag045
Dates: received 1 May 2025; accepted 5 March 2026; published online 9 March 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1093/braincomms/fcag045 · PMID 41809434 · PMCID PMC12967851 · OpenAlex W7134264201
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), other (modality), human (organism), other condition (population), stroke (population), clinical / translational (subfield)
Methods: Statistics, Preprocessing, Connectivity
Keywords: hospitalization, white matter hyperintensity, hippocampal subfield, glial fibrillary acidic protein, memory
Topic: Long-Term Effects of COVID-19 (Neurology, Medicine), according to OpenAlex
Funding: NIA NIH HHS (R01 AG063525, P30 AG066546, R01 AG056043, R56 AG074467); NHLBI NIH HHS (P01 HL040962); NIDDK NIH HHS (R01 DK110041)
Citations: cited by 1 paper (Europe PMC); 65 references in the paper
Research resources: RRID:SCR_022735

Abstract

We examined the impact of COVID-19 hospitalization on neuroimaging biomarkers and the association of these neuroimaging biomarkers with cognitive measures and plasma biomarkers. A total of 179 dementia-free people, including 52 hospitalized COVID-19 patients, across four medical centres in the USA and UK underwent 7T brain MRI scans, cognitive tests and blood collection. We found that hospitalized patients exhibited a comparable white matter hyperintensity burden, lower total hippocampal volume and lower plasma glial fibrillary acidic protein concentration, along with poorer memory performance, compared to age-matched non-hospitalized participants. Higher white matter hyperintensity burden was associated with older age, worse cognitive scores and higher plasma biomarker levels; higher total hippocampal volume was associated with younger age, better cognitive scores and lower plasma phosphorylated tau levels. However, these correlation coefficients did not differ between the hospitalized and non-hospitalized groups. Longitudinal studies are needed to clarify the long-term impact of COVID-19-related hospitalization.

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

Repositories

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

jinghangli98/wmh_seg

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: a5ad55c6dec7cb2d4bd7b419a3e7d0c14e72aaee, 25 May 2026
Languages: Python (8)
Size: 23 files, 8 scripts
Software Heritage: not archived
Found in: the text, “MRI harmonization, segmentation and quality cont”
Holds: README, environment (requirements.txt, setup.py)
Not found: license file, CITATION.cff, tests, continuous integration, documentation
Tools: NiBabel (6 files), NumPy (5 files), PyTorch (4 files), nnU-Net (2 files)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
9 files
At the source: github.com/jinghangli98/wmh_seg

pyushkevich/ashs

License: GPL-3.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 8dc72a2b7e96c19d64ef494890093b92ec2a10df, 9 March 2026
Languages: Shell (35), C/C++ (10), Perl (1)
Size: 164 files, 46 scripts
Software Heritage: archived
Found in: the text, “MRI harmonization, segmentation and quality cont”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ANTs (5 files), FSL (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
48 files
At the source: github.com/pyushkevich/ashs

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:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 54 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

All data generated and analysed during this study are included in this article. The anonymized raw and processed MRI scans, along with group-level plasma biomarkers and cognitive data, are available upon reasonable request. All GitHub codes used in this work are cited in the methods section.

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, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 31 authors, 5 keywords, 3 funders, 59 references, 1 RRID.

Cite

This paper

Liou, J.-J., Santini, T., Li, J., Gireud-Goss, M., Kautz, T. F., Parker-Garza, J., Guerrero, J. C., Patel, V., Adeyemi, O. F., de Erausquin, G. A., Garbarino, V. R., Habes, M., Himali, J. J., Karmonik, C., Snitz, B. E., Mettenburg, J. M., Wu, M., Aizenstein, H. J., Marsland, A. L., . . . 7T MRI COVID Consortium. (2026). Examining neuroimaging biomarkers, plasma biomarkers and cognitive functions in patients with recovered COVID-19 infection: a multicentre study using 7T MRI. Brain communications, 8(2), fcag045. https://doi.org/10.1093/braincomms/fcag045

BibTeX

@article{liou2026examining,
author = {Liou, Jr-Jiun and Santini, Tales and Li, Jinghang and Gireud-Goss, Monica and Kautz, Tiffany F and Parker-Garza, Julie and Guerrero, Juan Carlos and Patel, Vibhuti and Adeyemi, Oluwatobi F and de Erausquin, Gabriel A and Garbarino, Valentina R and Habes, Mohamad and Himali, Jayandra J and Karmonik, Christof and Snitz, Beth E and Mettenburg, Joseph M and Wu, Minjie and Aizenstein, Howard J and Marsland, Anna L and Gianaros, Peter J and Bowtell, Richard and Mougin, Olivier and Gowland, Penny A and Katshu, Mohammad Zia and Vahidy, Farhaan S and Girard, Timothy D and Jacobs, Heidi I L and Hosseini, Akram A and Seshadri, Sudha and Ibrahim, Tamer S and {7T MRI COVID Consortium}},
title = {{Examining neuroimaging biomarkers, plasma biomarkers and cognitive functions in patients with recovered COVID-19 infection: a multicentre study using 7T MRI}},
journal = {Brain communications},
year = {2026},
month = mar,
volume = {8},
number = {2},
pages = {fcag045},
publisher = {Oxford University Press},
issn = {2632-1297},
doi = {10.1093/braincomms/fcag045},
url = {https://doi.org/10.1093/braincomms/fcag045},
pmid = {41809434},
pmcid = {PMC12967851}
}

RIS

TY - JOUR
AU - Liou, Jr-Jiun
AU - Santini, Tales
AU - Li, Jinghang
AU - Gireud-Goss, Monica
AU - Kautz, Tiffany F
AU - Parker-Garza, Julie
AU - Guerrero, Juan Carlos
AU - Patel, Vibhuti
AU - Adeyemi, Oluwatobi F
AU - de Erausquin, Gabriel A
AU - Garbarino, Valentina R
AU - Habes, Mohamad
AU - Himali, Jayandra J
AU - Karmonik, Christof
AU - Snitz, Beth E
AU - Mettenburg, Joseph M
AU - Wu, Minjie
AU - Aizenstein, Howard J
AU - Marsland, Anna L
AU - Gianaros, Peter J
AU - Bowtell, Richard
AU - Mougin, Olivier
AU - Gowland, Penny A
AU - Katshu, Mohammad Zia
AU - Vahidy, Farhaan S
AU - Girard, Timothy D
AU - Jacobs, Heidi I L
AU - Hosseini, Akram A
AU - Seshadri, Sudha
AU - Ibrahim, Tamer S
AU - 7T MRI COVID Consortium
TI - Examining neuroimaging biomarkers, plasma biomarkers and cognitive functions in patients with recovered COVID-19 infection: a multicentre study using 7T MRI
T2 - Brain communications
J2 - Brain Commun
PY - 2026
DA - 2026/03/09
VL - 8
IS - 2
SP - fcag045
SN - 2632-1297
PB - Oxford University Press
DO - 10.1093/braincomms/fcag045
UR - https://doi.org/10.1093/braincomms/fcag045
LA - en
ER -

CSL-JSON

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