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Diffusivity anisotropy signature of slowly expanding lesions predicts progression independent of relapse activity in multiple sclerosis.

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Paper

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The authors' code

Shell · 46 lines · 1.3 KB · Apache-2.0

  1. #!/usr/bin/env bash
  2. # safe-label.sh — label wrapper with a denylist.
  3. #
  4. # Usage: safe-label.sh <number> <add|remove> <label>
  5. #
  6. # Blocks the "ready-for-fix" label so agent workflows cannot apply it and
  7. # thereby trigger the bug-fix PR workflow. All other labels pass through.
  8. # The denylist is intentionally small; this is the structural boundary that
  9. # makes fix-PR creation a human-only decision.
  10. #
  11. # GITHUB_REPOSITORY is provided automatically by GitHub Actions.
  13. set -euo pipefail
  15. if [[ $# -ne 3 ]]; then
  16. echo "Usage: $0 <number> <add|remove> <label>" >&2
  17. exit 2
  18. fi
  20. NUMBER="$1"
  21. ACTION="$2"
  22. LABEL="$3"
  24. # Deny ADD of the ready-for-fix label. REMOVE is allowed so the fix
  25. # workflow can clear the label after opening its PR.
  26. case "$ACTION:$LABEL" in
  27. add:ready-for-fix)
  28. echo "safe-label.sh: refusing to add label 'ready-for-fix' — reserved for maintainers" >&2
  29. exit 1
  30. ;;
  31. esac
  33. REPO="${GITHUB_REPOSITORY:?GITHUB_REPOSITORY must be set}"
  35. case "$ACTION" in
  36. add)
  37. exec gh issue edit "$NUMBER" --repo "$REPO" --add-label "$LABEL"
  38. ;;
  39. remove)
  40. exec gh issue edit "$NUMBER" --repo "$REPO" --remove-label "$LABEL"
  41. ;;
  42. *)
  43. echo "safe-label.sh: unknown action '$ACTION' (expected add|remove)" >&2
  44. exit 2
  45. ;;
  46. esac

safe-label.sh at commit 202f6ba, under Apache-2.0 · at the source

Overview

Authors: Alberto Calvi1, Francesc Vivó Pascual1, Elisabeth Solana1, Elisabet Lopez-Soley1, Baris Kanber2,3,4, Salut Alba-Arbalat1, Maria Sepulveda1, Eugenia Martínez-Hernández1, José Maria Cabrera-Maqueda1, Elianet Fonseca1, Santiago Medrano-Martorell5, Albert Saiz1, Yolanda Blanco1, Pablo Villoslada6, Ferran Prados Carrasco2,4,7, Eloy Martinez-Heras1, Sara Llufriu1
ORCID iDs: Alberto Calvi, Francesc Vivó Pascual, Elisabeth Solana, Baris Kanber, Salut Alba-Arbalat, Eugenia Martínez-Hernández, Elianet Fonseca, Ferran Prados Carrasco, Eloy Martinez-Heras, Sara Llufriu
  1. Neuroimmunology and Multiple Sclerosis Unit and Laboratory of Advanced Imaging in Neuroimmunological Diseases (ImaginEM), Hospital Clinic Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
  2. Institute of Neurology, Faculty of Brain Sciences, University College London (UCL), London, UK
  3. Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London (UCL), London, UK
  4. National Institute for Health Research (NIHR), University College London Hospitals (UCLH), Biomedical Research Centre, London, UK
  5. Neuroradiology Department, Centre de Diagnòstic per la Imatge (CDI), Hospital Clinic Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
  6. Department of Neurology, Hospital del Mar, Pompeu Fabra University, Barcelona, Spain
  7. e-Health Centre, Universitat Oberta de Catalunya, Barcelona, Spain
Institutions: Hospital Clínic de Barcelona (Spain); Consorci Institut D'Investigacions Biomediques August Pi I Sunyer (Spain); Universitat de Barcelona (Spain); National Institute for Health and Care Research (United Kingdom); UCL Biomedical Research Centre (United Kingdom); UCL Queen Square Institute of Neurology (United Kingdom); University College London (United Kingdom); Universitat Pompeu Fabra (Spain); Hospital Del Mar (Spain); Universitat Oberta de Catalunya (Spain)
Journal: Journal of neurology, neurosurgery, and psychiatry, volume 97, issue 5, article e335884
Dates: received 22 January 2025; accepted 30 July 2025; published online 1 September 2025
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1136/jnnp-2025-335884 · PMID 40897401 · PMCID PMC13151513 · OpenAlex W4413933690
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), human (organism), multiple sclerosis (population), clinical / translational (subfield)
Methods: Statistics, Preprocessing, Connectivity, Machine learning, fMRI & imaging
Keywords: MRI, MULTIPLE SCLEROSIS
MeSH: Brain*, Multiple Sclerosis*, Adult, Anisotropy, Diffusion Magnetic Resonance Imaging, Disease Progression, Female, Humans, Male, Middle Aged, Prospective Studies, Recurrence (* major topic)
Journal subjects: Multiple Sclerosis
Topic: Multiple Sclerosis Research Studies (Pathology and Forensic Medicine, Medicine), according to OpenAlex
Funding: Red Española de Esclerosis Múltiple (N/A); Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III) (PI21/01189, PI24/00567); European Committee for Treatment and Research in Multiple Sclerosis (N/A); Bristol Myers Squibb Foundation (N/A); Agencia de Gestio d'Ajuts Universitaris i de Recerca (021-SGR-01325); Fundacion BBVA (N/A)
Citations: cited by 5 papers (Europe PMC); 40 references in the paper

Abstract

Background: Slowly expanding lesions (SELs) in multiple sclerosis (MS) are markers of chronic active lesions and seem to trigger disability. This study aimed to analyse spatial features of SELs through diffusion MRI and their clinical impact on progression independent of relapse activity (PIRA).

Methods: An observational study of MS subjects prospectively followed since 2011; inclusion required at least three longitudinal T1/T2-weighted and diffusion-weighted MRIs. Subjects followed clinical assessments, using Multiple Sclerosis Functional Composite (MSFC) and Expanded Disability Status Scale. At MRI, lesions were categorised using non-linear deformation as definite or possible SELs, and non-SELs. Fractional anisotropy (FA) was extracted from each lesion core and perilesional area. Differences in FA values across core and perilesional areas by SEL category were assessed using the Mann-Whitney test. Associations with PIRA and clinical outcomes were evaluated using mixed-effects, logistic and Cox regression models.

Results: 130 subjects underwent MRI (median 25 months) and clinical assessments (median follow-up 9.2 years), of which 29 (22%) developed PIRA. Of 4811 lesions, 8% were definite SELs. Definite SELs exhibited FA decline over time in core and perilesional areas compared with other lesions. Longitudinal core FA reductions within definite SELs were associated with worse MSFC z-score evolution (β=0.03, 95% CI 0.01 to 0.05, p=0.003), higher odds for PIRA (OR=0.01, 95% CI 0.01 to 0.12, p=0.001) and predicted faster time to reach first PIRA event (HR=0.03, 95% CI 0 to 0.49, p=0.015).

Conclusions: Definite SELs show distinct greater microstructural damage and are associated with PIRA, making their FA signature a potential predictor of MS progression.

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

Repository

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

MIC-DKFZ/nnUNet

License: Apache-2.0
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 202f6baa0adc2ef5f7b615df19cc4da970412cc0, 25 September 2026
Languages: Python (216), Shell (7)
Size: 303 files, 223 scripts
Software Heritage: archived
Found in: the text, “Lesion segmentation and perilesional area defini”
Holds: README, license file, environment (pyproject.toml, setup.py), tests, continuous integration, documentation
Not found: CITATION.cff
Tools: nnU-Net (125 files), NumPy (73 files), PyTorch (56 files), SimpleITK (10 files), scikit-image (6 files), SciPy (5 files), NiBabel (4 files), pandas (4 files), tifffile (3 files), Matplotlib (2 files), scikit-learn (1 file), seaborn (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
225 files
At the source: github.com/MIC-DKFZ/nnUNet

Tracing map

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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

Imaging data in Brain Imaging Data Structure (BIDS) format and the clinical data supporting the findings of this research can be accessed on reasonable request to the corresponding authors.

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

Data availability statement

Data are available upon reasonable request.

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

Versions

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Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 17 authors, 2 keywords, 12 MeSH terms, 6 funders, 38 references.

Cite

This paper

Calvi, A., Vivó Pascual, F., Solana, E., Lopez-Soley, E., Kanber, B., Alba-Arbalat, S., Sepulveda, M., Martínez-Hernández, E., Cabrera-Maqueda, J. M., Fonseca, E., Medrano-Martorell, S., Saiz, A., Blanco, Y., Villoslada, P., Prados Carrasco, F., Martinez-Heras, E., & Llufriu, S. (2026). Diffusivity anisotropy signature of slowly expanding lesions predicts progression independent of relapse activity in multiple sclerosis. Journal of neurology, neurosurgery, and psychiatry, 97(5), e335884. https://doi.org/10.1136/jnnp-2025-335884

BibTeX

@article{calvi2026diffusivity,
author = {Calvi, Alberto and Vivó Pascual, Francesc and Solana, Elisabeth and Lopez-Soley, Elisabet and Kanber, Baris and Alba-Arbalat, Salut and Sepulveda, Maria and Martínez-Hernández, Eugenia and Cabrera-Maqueda, José Maria and Fonseca, Elianet and Medrano-Martorell, Santiago and Saiz, Albert and Blanco, Yolanda and Villoslada, Pablo and Prados Carrasco, Ferran and Martinez-Heras, Eloy and Llufriu, Sara},
title = {{Diffusivity anisotropy signature of slowly expanding lesions predicts progression independent of relapse activity in multiple sclerosis}},
journal = {Journal of neurology, neurosurgery, and psychiatry},
year = {2026},
month = apr,
volume = {97},
number = {5},
pages = {e335884},
publisher = {BMJ},
issn = {0022-3050},
doi = {10.1136/jnnp-2025-335884},
url = {https://doi.org/10.1136/jnnp-2025-335884},
pmid = {40897401},
pmcid = {PMC13151513}
}

RIS

TY - JOUR
AU - Calvi, Alberto
AU - Vivó Pascual, Francesc
AU - Solana, Elisabeth
AU - Lopez-Soley, Elisabet
AU - Kanber, Baris
AU - Alba-Arbalat, Salut
AU - Sepulveda, Maria
AU - Martínez-Hernández, Eugenia
AU - Cabrera-Maqueda, José Maria
AU - Fonseca, Elianet
AU - Medrano-Martorell, Santiago
AU - Saiz, Albert
AU - Blanco, Yolanda
AU - Villoslada, Pablo
AU - Prados Carrasco, Ferran
AU - Martinez-Heras, Eloy
AU - Llufriu, Sara
TI - Diffusivity anisotropy signature of slowly expanding lesions predicts progression independent of relapse activity in multiple sclerosis
T2 - Journal of neurology, neurosurgery, and psychiatry
J2 - J Neurol Neurosurg Psychiatry
PY - 2026
DA - 2026/04/15
VL - 97
IS - 5
SP - e335884
SN - 0022-3050
PB - BMJ
DO - 10.1136/jnnp-2025-335884
UR - https://doi.org/10.1136/jnnp-2025-335884
LA - en
ER -

CSL-JSON

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