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Gray Matter Microstructure Measured Using Diffusion Imaging as a Biomarker of Severity in Lewy Body Diseases.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches · all tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Image Acquisition and Preprocessing ↔ CODE/Step1a_PreprocessMPRAGE.sh, the whole file · a weak match · score 0.63 · brain mask, FreeSurfer, Synthstrip, space, preprocessed, MRI
  2. [2] § Methods › NODDI Calculation ↔ CODE/Step1c_GetTissueFractionMaps.sh, the whole file · a weak match · score 0.56 · tissue fraction map, fitted, mask, AMICO, NODDI, NDI

Paper

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

The paper is loaded when this pane is shown.

The authors' code

Shell · 26 lines · 1.3 KB · CC0-1.0 · 1 match

  1. basedir="/mnt/y/PROJECTS/GMmicrostructure/DATA"
  3. #basedir="/mnt/y/PROJECTS/GMmicrostructure/DATA/Longitudinal_VIPD/SESSION2"
  4. mapfile -t allsubs < ../DATA/Batch.txt
  5. cd ${basedir}
  6. #allsubs=("VIPD_007")
  7. for sub in "${allsubs[@]}"; do
  8. subdir=$basedir/$sub
  9. cd $subdir
  10. echo $sub
  11. # Create T1 segmentations and mask
  12. mri_synthstrip -i T1.nii.gz -o T1_brain_masked.nii.gz -m T1_brain.nii.gz
  13. fast -n 3 -o T1_seg T1.nii.gz
  14. fslmaths T1_seg_pve_1.nii.gz -mas T1_brain.nii.gz -thr 0.5 -bin T1_GM.nii.gz
  16. # Coregister to the DWI
  17. reg_aladin -ref b0.nii.gz -flo T1.nii.gz -res T1_in_DWIspace.nii.gz -aff T1_to_DWI_aff.txt
  18. reg_resample -ref b0.nii.gz -flo T1_brain.nii.gz -trans T1_to_DWI_aff.txt -res DWI_brain.nii.gz -inter 0
  19. reg_resample -ref b0.nii.gz -flo T1_GM.nii.gz -trans T1_to_DWI_aff.txt -res GM_mask.nii.gz -inter 0
  21. # # Shaefer parcellation to T1
  22. reg_aladin -ref T1.nii.gz -flo $basedir/MNI152_T1_1mm.nii.gz -res MNI152_in_T1space.nii.gz -aff MNI_to_T1_aff.txt
  23. reg_resample -ref T1.nii.gz -flo $basedir/Schaefer2018_232Parcels_7Networks_order_FSLMNI152_1mm.nii.gz -trans MNI_to_T1_aff.txt -res Schaefer232_T1space.nii.gz -aff MNI_to_T1_aff.txt -inter 0
  24. reg_resample -ref b0.nii.gz -flo Schaefer232_T1space.nii.gz -res Schaefer232_DWIspace.nii.gz -trans T1_to_DWI_aff.txt -inter 0
  26. done

Step1a_PreprocessMPRAGE.sh at commit 6eea9bc, under CC0-1.0 · at the source

Overview

Authors: Angeliki Zarkali MBBS, PhD1,2,3,4, Ivelina Dobreva MSc1, Naomi Hannaway MSc1, Rohan Bhome MBBS, PhD1, George E.C. Thomas PhD1, Steffani Carrera MSc1, Amanda J. Heslegrave PhD5, Elena Veleva PhD5, Henrik Zetterberg PhD1,5, Rimona S. Weil MBBS, PhD1,2,3,4
ORCID iDs: Angeliki Zarkali MBBS, PhD, Ivelina Dobreva MSc, Naomi Hannaway MSc, Rohan Bhome MBBS, PhD, Rimona S. Weil MBBS, PhD
  1. Dementia Research Centre, UCL Queen Square Institute of Neurology University College London London United Kingdom
  2. National Hospital for Neurology and Neurosurgery London United Kingdom
  3. Movement Disorders Centre, UCL Queen Square Institute of Neurology University College London London United Kingdom
  4. Department of Imaging Neuroscience, UCL Queen Square Institute of Neurology University College London London United Kingdom
  5. UK DRI Fluid Biomarker Lab and Biomarker Factory University College London London United Kingdom
Institutions: National Hospital for Neurology and Neurosurgery (United Kingdom); UCL Queen Square Institute of Neurology (United Kingdom); University College London (United Kingdom)
Journal: Movement disorders : official journal of the Movement Disorder Society, volume 41, issue 9, pages 2310-2324
Dates: received 26 February 2026; accepted 30 April 2026; published online 25 May 2026; in print September 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1002/mds.70355 · PMID 42185748 · PMCID PMC13602283 · OpenAlex W7162337539
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), human (organism), Alzheimer's / dementia (population), Parkinson's (population), clinical / translational (subfield)
Methods: Statistics, fMRI & imaging, Preprocessing
Keywords: diffusion‐weighted imaging, gray matter microstructure, Lewy body dementia, Lewy body diseases, neuroimaging, Parkinson's disease
MeSH: Diffusion Magnetic Resonance Imaging*, Gray Matter*, Lewy Body Disease*, Parkinson Disease*, Aged, Aged, 80 and over, Biomarkers, Cross-Sectional Studies, Female, Humans, Longitudinal Studies, Male, Middle Aged, Severity of Illness Index (* major topic)
Topic: Parkinson's Disease Mechanisms and Treatments (Neurology, Medicine), according to OpenAlex
Funding: UK Research and Innovation Future (UKRI2343); Wellcome Trust (225263/Z/22); Rosetrees Trust; Academy of Medical Sciences; Parkinson's UK
Citations: not cited yet (Europe PMC); 81 references in the paper

Abstract

Background: Despite widespread cortical involvement in Lewy body diseases, conventional gray matter magnetic resonance imaging (MRI) shows limited sensitivity. Diffusion‐weighted MRI‐derived microstructural measures have shown utility in Alzheimer's disease, but their application across the Lewy body disease spectrum remains limited.

Objectives: The goal was to examine gray matter microstructure in 197 participants across the Lewy body disease spectrum (88 Lewy body dementia [LBD], 109 Parkinson's disease, and normal cognition [PD‐NC]) and 46 controls.

Methods: Tissue‐weighted neurite density index, tissue‐weighted orientation dispersion index, and free water fraction were examined across 200 cortical and 32 subcortical regions. We compared these cross‐sectionally between LBD, PD‐NC and controls, and longitudinally over 3 years in a subset of 100 patients with Parkinson's disease cognitively intact at baseline. We assess associations with disease severity and plasma p‐tau217 levels.

Results: LBD showed widespread cortical and subcortical increases in free water fraction and, to lesser extent, orientation dispersion compared to controls and PD‐NC, despite minimal atrophy and no neurite density differences. In temporoparietal regions, increases in free water fraction and orientation dispersion correlated with cognitive, but not motor, severity, and with plasma p‐tau217. Longitudinally, Parkinson's disease patients who developed cognitive impairment showed greater free water fraction increases within bilateral temporal regions, right thalamus, and right caudate.

Conclusions: Diffusion‐derived microstructural measures, particularly free water fraction are sensitive to early and progressive gray matter changes associated with cognitive decline in Lewy body diseases. Findings suggest microstructural disruption without overt neuronal loss and support free water fraction as a potential biomarker for disease staging and progression. © 2026 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

AngelikaZa/GM_Microstructure

License: CC0-1.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 6eea9bc52696967a2a8391668943528f11b14cfb, 18 May 2026
Languages: Shell (5), Python (5)
Size: 18 files, 10 scripts
Software Heritage: not archived
Found in: “Data Sharing”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: pandas (5 files), FSL (3 files), NiBabel (3 files), BrainSpace (2 files), FreeSurfer (2 files), NumPy (2 files), Connectome Workbench (2 files), Nilearn (1 file)
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
12 files
At the source: github.com/AngelikaZa/GM_Microstructure

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:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 10 scripts, each with its path and the digest of its content;
  • 2 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 data that support the findings of this study are available on request from the corresponding author. The data are not publicly available due to privacy or ethical restrictions.

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

Data Sharing

Processing and analysis code and anonymized group‐level data will be available on publication through https://github.com/AngelikaZa/GM_Microstructure. Individual‐level and raw imaging data may be shared on reasonable request to the corresponding author.

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 2, 28 September 2026

  • Publisher: n/a → Wiley

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 10 authors, 6 keywords, 14 MeSH terms, 5 funders, 79 references.

Cite

This paper

Zarkali, A., Dobreva, I., Hannaway, N., Bhome, R., Thomas, G. E., Carrera, S., Heslegrave, A. J., Veleva, E., Zetterberg, H., & Weil, R. S. (2026). Gray Matter Microstructure Measured Using Diffusion Imaging as a Biomarker of Severity in Lewy Body Diseases. Movement disorders : official journal of the Movement Disorder Society, 41(9), 2310-2324. https://doi.org/10.1002/mds.70355

BibTeX

@article{zarkali2026gray,
author = {Zarkali, Angeliki and Dobreva, Ivelina and Hannaway, Naomi and Bhome, Rohan and Thomas, George E.C. and Carrera, Steffani and Heslegrave, Amanda J. and Veleva, Elena and Zetterberg, Henrik and Weil, Rimona S.},
title = {{Gray Matter Microstructure Measured Using Diffusion Imaging as a Biomarker of Severity in Lewy Body Diseases}},
journal = {Movement disorders : official journal of the Movement Disorder Society},
year = {2026},
month = may,
volume = {41},
number = {9},
pages = {2310--2324},
publisher = {Wiley},
issn = {0885-3185},
doi = {10.1002/mds.70355},
url = {https://doi.org/10.1002/mds.70355},
pmid = {42185748},
pmcid = {PMC13602283}
}

RIS

TY - JOUR
AU - Zarkali, Angeliki
AU - Dobreva, Ivelina
AU - Hannaway, Naomi
AU - Bhome, Rohan
AU - Thomas, George E.C.
AU - Carrera, Steffani
AU - Heslegrave, Amanda J.
AU - Veleva, Elena
AU - Zetterberg, Henrik
AU - Weil, Rimona S.
TI - Gray Matter Microstructure Measured Using Diffusion Imaging as a Biomarker of Severity in Lewy Body Diseases
T2 - Movement disorders : official journal of the Movement Disorder Society
J2 - Mov Disord
PY - 2026
DA - 2026/05/25
VL - 41
IS - 9
SP - 2310
EP - 2324
SN - 0885-3185
PB - Wiley
DO - 10.1002/mds.70355
UR - https://doi.org/10.1002/mds.70355
LA - en
ER -

CSL-JSON

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