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Distinct brain regions are affected by neurodevelopmental or pre-dementia changes in Down syndrome.

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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

MATLAB · 55 lines · 1.4 KB · no license

  1. function [a, f] = myGetTotals_Mean_v2(files, msk)
  4. % Script adapted from Ged Ridgway's MATLAB script: http://www0.cs.ucl.ac.uk/staff/g.ridgway/vbm/get_totals.m
  6. % The script returns the average voxel value (`a`) within a binary mask (`msk`) for the image listed in `file`.
  8. % The masking process assumes that the `msk` matches the voxel dimensions of each image; therefore, the image and mask must share the same dimensions.
  11. % Example usage
  12. %[a01, f01] = myGetTotals_Mean('GM_map01_mni.nii', 'mask01_mni.nii');
  13. %[a02, f02] = myGetTotals_Mean('GM_map02_mni.nii', 'mask02_mni.nii');
  16. % check spm version:
  17. if exist('spm_select','file') % should be true for spm5
  18. spm5 = 1;
  19. select = @(msg) spm_select(inf, 'image', msg);
  20. elseif exist('spm_get','file') % should be true for spm2
  21. spm5 = 0;
  22. select = @(msg) spm_get(inf, 'img', msg);
  23. else
  24. error('Failed to locate spm_get or spm_select; please add SPM to Matlab path')
  25. end
  27. if ( ~exist('files', 'var') || isempty(files) )
  28. files = select('choose images');
  29. end
  31. if ~exist('msk', 'var')
  32. msk = 1; % default to include everything
  33. end
  34. if isempty(msk)
  35. msk = select('Choose mask image');
  36. end
  37. if ischar(msk)
  38. msk = spm_vol(msk);
  39. end
  40. if isstruct(msk)
  41. msk = spm_read_vols(msk);
  42. end
  43. msk = msk ~= 0;
  45. vols = spm_vol(files);
  46. N = length(vols);
  48. f=files;
  50. a = zeros(N,1);
  51. for n = 1:N
  52. img = spm_read_vols(vols(n));
  53. img = img .* msk;
  54. a(n) = sum(img(img > 0))/size(find(img > 0),1);
  55. end

myGetTotals_Mean_v2.m at commit 7dd66c2, no license · at the source

Overview

Authors: Lília Jorge1,2,3, Joana Oliveira1,3,4, Ricardo Martins1,3, Tânia Lopes1,3, Hugo Quental1,3, Miguel Castelo-Branco1,3,4
ORCID iDs: Ricardo Martins, Miguel Castelo-Branco
  1. Institute for Nuclear Sciences Applied to Health, University of Coimbra, 3000-548 Coimbra, Portugal
  2. Faculty of Science and Technology, University of Coimbra, 3030-790 Coimbra, Portugal
  3. Coimbra Institute for Biomedical Imaging and Translational Research, 3000-548 University of Coimbra, Coimbra, Portugal
  4. Institute for Physiology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
Institutions: University of Coimbra (Portugal)
Journal: Brain communications, volume 8, issue 4, article fcag269
Dates: received 2 January 2026; accepted 3 June 2026; published online 13 July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1093/braincomms/fcag269 · PMID 42488757 · PMCID PMC13390646 · OpenAlex W7168189087
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), other condition (population), Alzheimer's / dementia (population)
Methods: Statistics, Preprocessing, Connectivity, fMRI & imaging
Keywords: Down syndrome, structural MRI, neurodevelopment, episodic memory, Alzheimer’s disease
Topic: Down syndrome and intellectual disability research (Public Health, Environmental and Occupational Health, Medicine), according to OpenAlex
Funding: Foundation for Science and Technology; FCT (FCT/UID/4950/2025, CENTRO2030-FEDER-02595800_MedImSig)
Citations: not cited yet (Europe PMC); 144 references in the paper

Abstract

Down syndrome, a condition characterized by triplication of chromosome 21, leads to a complex interplay between neurodevelopmental and dementia-related changes similar to the ones observed in Alzheimer’s disease. Here we aimed to understand this interplay by using imaging biomarkers for different cognitive profiles in Down syndrome, and by analysing early developmental differences versus age-related changes. We analysed voxel-based morphometric measures of grey matter volume from high-resolution T1-weighted MRI in 23 adults with Down syndrome (18–59 years, five female) in preclinical/prodromal stages of Alzheimer’s disease and 24 age- and sex-matched controls, along with cognitive assessments. Neuroanatomical group differences were assessed using two-sample t-tests. Age-related effects on brain integrity, and cognitive function were examined through voxel-wise regression analyses and correlation tests, respectively. Finally, structural correlates of episodic memory were explored across the whole brain at the voxel level within the Down syndrome group. Results revealed a neuroanatomic phenotype with both regional increases and decreases in grey matter volume compared to controls (false discovery rate, q ≤ 0.05). Based on regression analysis, we found the following patterns in regions that were differentially reduced in Down syndrome: same intercept and different age-related slope (defining specific age-related differences), different intercept (implying initial neurodevelopmental differences) and same slope (signalling no age-related differences). A notable example of the first was the left hippocampus and its subfields, and of the second was the orbitofrontal cortex. Follow-up whole brain analyses confirmed age-related changes in Down syndrome (false discovery rate, q ≤ 0.05) in the parietal and temporal cortices, extending into hippocampus, as compared to controls, independent of neurodevelopmental (non-age related) features, and most pronounced in the right hemisphere. Episodic and associative memory declined significantly with age (P = 0.016) in Down syndrome and correlated with shrinkage in regions vulnerable to Alzheimer’s disease (P < 0.01), including the precuneus and posterior cingulate cortex. Our findings suggest that individuals with Down syndrome undergo early brain atrophy that occurs independently of baseline neurodevelopmental changes, particularly in the hippocampus and temporoparietal regions. Notably the posterior cingulate cortex and precuneus showed an association with episodic memory loss, a pattern that is consistent with Alzheimer’s Disease. In sum we found a dichotomic distinction between brain regions affected by developmental or ageing changes in Down syndrome.

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

Repository

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

ricardomar/Lilia-journal-2026

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 7dd66c23319be82423a41b385b968ee4807bf943, 23 March 2026
Languages: MATLAB (1)
Size: 2 files, 1 script
Software Heritage: not archived
Found in: “Data availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: SPM (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
2 files
At the source: github.com/ricardomar/Lilia-journal-2026

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;
  • 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

The data supporting the current findings are available from the corresponding author upon reasonable request. The in-house MATLAB script used to extract mean GM volumes in the ROIs of interest is publicly available in an online repository at the following link: https://github.com/ricardomar/Lilia-journal-2026.

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, 6 authors, 5 keywords, 2 funders, 135 references.

Cite

This paper

Jorge, L., Oliveira, J., Martins, R., Lopes, T., Quental, H., & Castelo-Branco, M. (2026). Distinct brain regions are affected by neurodevelopmental or pre-dementia changes in Down syndrome. Brain communications, 8(4), fcag269. https://doi.org/10.1093/braincomms/fcag269

BibTeX

@article{jorge2026distinct,
author = {Jorge, Lília and Oliveira, Joana and Martins, Ricardo and Lopes, Tânia and Quental, Hugo and Castelo-Branco, Miguel},
title = {{Distinct brain regions are affected by neurodevelopmental or pre-dementia changes in Down syndrome}},
journal = {Brain communications},
year = {2026},
month = jul,
volume = {8},
number = {4},
pages = {fcag269},
publisher = {Oxford University Press},
issn = {2632-1297},
doi = {10.1093/braincomms/fcag269},
url = {https://doi.org/10.1093/braincomms/fcag269},
pmid = {42488757},
pmcid = {PMC13390646}
}

RIS

TY - JOUR
AU - Jorge, Lília
AU - Oliveira, Joana
AU - Martins, Ricardo
AU - Lopes, Tânia
AU - Quental, Hugo
AU - Castelo-Branco, Miguel
TI - Distinct brain regions are affected by neurodevelopmental or pre-dementia changes in Down syndrome
T2 - Brain communications
J2 - Brain Commun
PY - 2026
DA - 2026/07/13
VL - 8
IS - 4
SP - fcag269
SN - 2632-1297
PB - Oxford University Press
DO - 10.1093/braincomms/fcag269
UR - https://doi.org/10.1093/braincomms/fcag269
LA - en
ER -

CSL-JSON

{
"id": "10.1093/braincomms/fcag269",
"type": "article-journal",
"title": "Distinct brain regions are affected by neurodevelopmental or pre-dementia changes in Down syndrome",
"container-title": "Brain communications",
"author": [
{
"family": "Jorge",
"given": "Lília"
},
{
"family": "Oliveira",
"given": "Joana"
},
{
"family": "Martins",
"given": "Ricardo"
},
{
"family": "Lopes",
"given": "Tânia"
},
{
"family": "Quental",
"given": "Hugo"
},
{
"family": "Castelo-Branco",
"given": "Miguel"
}
],
"container-title-short": "Brain Commun",
"volume": "8",
"issue": "4",
"page": "fcag269",
"DOI": "10.1093/braincomms/fcag269",
"PMID": "42488757",
"PMCID": "PMC13390646",
"ISSN": "2632-1297",
"publisher": "Oxford University Press",
"URL": "https://doi.org/10.1093/braincomms/fcag269",
"language": "en",
"issued": {
"date-parts": [
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2026,
7,
13
]
]
}
}

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