OSCR

Substantia Nigra MRI markers are lower in Alzheimer's disease and are linked to general cognitive function.

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

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

MATLAB · 24 lines · 1.1 KB · no license

  1. function calculate_diag_grp_diff_covars
  2. load CompleteData.mat
  3. covars={'dprime_new','NPT_global_score','age','sex','edyears','EstimatedTotalIntraCranialVol','WM','LAN','MEM','EXEC','VIS','totaltau','ratio_Abeta42_40_prec','phosphotau181'};
  4. statstbl=cell2table(cell(length(covars),1),"RowNames",covars,'VariableNames',{'result'});
  5. for a=1:length(covars)
  6. [~,b,c]=anova1(CompleteData.(covars{a}),CompleteData.diag,'off');
  7. F=round(b{contains(b(:,1),'Groups'),strcmp(b(1,:),'F')},2);
  8. p=round(b{contains(b(:,1),'Groups'),strcmp(b(1,:),'Prob>F')},2);
  9. diff=round(c.means(4)-c.means(1),2);
  10. statstbl{covars{a},1}={['F(3,156)=',num2str(F),', p=',num2str(p)]};
  11. end
  12. writetable(statstbl,'diagres_copy_paste.xlsx','WriteRowNames',true);
  14. for a=1:length(covars)
  15. [~,b,c]=anova1(CompleteData.(covars{a}),CompleteData.diag,'off');
  16. F=round(b{contains(b(:,1),'Groups'),strcmp(b(1,:),'F')},2);
  17. p=round(b{contains(b(:,1),'Groups'),strcmp(b(1,:),'Prob>F')},2);
  18. diff=round(c.means(4)-c.means(1),2);
  19. statstbl{covars{a},1}={['F(3,156)=',num2str(F),', p=',num2str(p),', AD-HC=',num2str(diff)]};
  20. end
  22. writetable(statstbl,'diagres.xlsx','WriteRowNames',true);
  24. end

calculate_diag_grp_diff_covars.m at commit 0c071eb, no license · at the source

Overview

Authors: Friedrich Krohn1, Mousumi Sarkar1, Hartmut Schütze1, Panagiotis Iliopoulos1, Lucía Penalba-Sánchez1,2, Dorothea Hämmerer1,2, Renat Yakupov1,2, Falk Lüsebrink1, Annika Spottke3, Anja Schneider3,4, Nina Roy3,4, Enise Incesoy1,2,5, Michael Heneka3,6, Ingo Kilimann7, Luca Kleineidam3,4, Stefan J Teipel7, Frederic Brosseron3, Doreen Goerss3,4, Wenzel Glanz1,2, Matthias Schmid8
and 6 other authorsAyda Rostamzadeh9, Michael Wagner3,4, Klaus Fliessbach3,4, Frank Olaf Jessen10, Emrah Düzel1,2, Matthew J Betts1,2
ORCID iDs: Friedrich Krohn, Renat Yakupov, Michael Heneka, Emrah Düzel
  1. Institute of Cognitive Neurology and Dementia Research (IKND), Otto-von-Guericke University, Magdeburg 39120, Germany
  2. Betts Group, German Center for Neurodegenerative Diseases, Magdeburg 39120, Germany
  3. Leitung klinische Forschung, German Center for Neurodegenerative Diseases, Bonn 53127, Germany
  4. Department of Old Age Psychiatry and Cognitive Disorders, 53127 University Hospital Bonn, Bonn, Germany
  5. Department for Psychiatry and Psychotherapy, University Clinic Magdeburg, 39120 Magdeburg, Germany
  6. Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux 4367, Luxembourg
  7. Klinische Demenzforschung, German Center for Neurodegenerative Diseases, Rostock 18147, Germany
  8. Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn 53127, Germany
  9. Department of Psychiatry, Medical Faculty, University of Cologne, Cologne 50924, Germany
  10. Faculty of Medicine, University of Cologne, Cologne 50932, Germany
Institutions: Otto-von-Guericke-Universität Magdeburg (Germany); German Center for Neurodegenerative Diseases (Germany); University Hospital Bonn (Germany); University Hospital Magdeburg (Germany); University of Luxembourg (Luxembourg); Luxembourg Centre for Systems Biomedicine (Luxembourg); University of Bonn (Germany); Institut für Medizinische Biometrie, Informatik und Epidemiologie (Germany); University of Cologne (Germany)
Journal: Brain communications, volume 8, issue 4, article fcag238
Dates: received 22 October 2024; accepted 4 April 2026; published online 24 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1093/braincomms/fcag238 · PMID 42488758 · PMCID PMC13390642 · OpenAlex W7165726884
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), human (organism), Alzheimer's / dementia (population), cognitive (subfield)
Methods: Connectivity, Statistics, fMRI & imaging
Keywords: Substantia Nigra (SN), Alzheimer's disease, neuromelanin, memory, novelty
Topic: Dementia and Cognitive Impairment Research (Psychiatry and Mental health, Medicine), according to OpenAlex
Funding: Deutsche Forschungsgemeinschaft (425899996); Deutsches Zentrum für Neurodegenerative Erkrankungen (BN012); Otto von Guericke University Magdeburg
Citations: not cited yet (Europe PMC); 98 references in the paper

Abstract

Individuals with Alzheimer’s disease dementia show Alzheimer's disease pathology and a heterogeneous degeneration of the Substantia Nigra (SN) post-mortem. However, it is unclear how SN degeneration is related to cognitive dysfunction across the Alzheimer’s disease dementia continuum. In this study, using data from the prospective DZNE-Longitudinal Cognitive Impairment and Dementia Study (DELCODE), we investigated whether in vivo SN MRI measures are lower in individuals with clinically defined Alzheimer’s disease dementia than in healthy control subjects (HC) and if they are associated with hippocampal functional activity during the processing of novel visual stimuli and subsequent recognition memory. One hundred and sixty DELCODE participants (69 years ± 6 years, 88 men), including 79 HC, 70 individuals with subjective cognitive decline (SCD), 17 individuals with mild cognitive impairment (MCI) and 10 individuals with Alzheimer’s disease dementia, completed a scene novelty and encoding task and a 3T SN-sensitive MRI scan, from which the two in vivo SN measures MRI contrast and volume were calculated and harmonized between scanner sites while preserving diagnostic group differences. For 71 individuals, CSF levels of phosphoTau, total tau and amyloid-beta 42/40 ratio (Aß42/40) were available. All individuals completed a neuropsychological task battery from which a global cognitive score was calculated. In separate models, we assessed the relationship between SN MRI markers and CSF levels of Alzheimer’s disease, the global cognitive score, hippocampal novelty activation and recognition memory while accounting for age, sex, years of education and total intracranial volume (TIV). SN volume but not SN MRI contrast was lower in individuals with clinical Alzheimer’s disease dementia [one-way analyses of covariance (ANCOVA); F(156,4) = 5.6665, P = 0.0010, n = 160]. SN MRI contrast and volume were not associated with Aß42/40, ptau and total tau CSF levels (all P > 0.1) or hippocampal novelty activation (all P > 0.1). Moreover, SN volume was positively associated with recognition memory (R2 = 0.07, P < 0.001, n = 159), global cognition (R2= 0.38, P < 0.0001, n = 160) and years of education (R2 = 0.03, P = 0.036, n = 160). Our study emphasizes the potential of using in vivo SN MRI markers to study the impact of SN degeneration on general cognitive impairment and recognition memory in an Alzheimer’s disease dementia cohort. Our results motivate future longitudinal studies to explore how SN volume and SN contrast change with disease progression, how these are differentially associated with cognitive decline, and how SN volume and SN contrast might be related to other dopamine-dependent cognitive functions and dysfunctions.

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

Repository

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

frikro/SN-Novelty-Brain-Comm

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 0c071ebcf485fbca719ce384e8ddbe1c75aec56d, 9 December 2025
Languages: MATLAB (6), Python (1)
Size: 8 files, 7 scripts
Software Heritage: not archived
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Statistics and Machine Learning Toolbox (3 files), SPM (2 files), pandas (1 file), Pingouin (1 file), statsmodels (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
7 files
At the source: github.com/frikro/SN-Novelty-Brain-Comm

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;
  • 7 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

Data, study protocol and biomaterials can be shared with partners based on individual data and biomaterial transfer agreements. Scripts used for data analyses of this manuscript can be found here: https://github.com/frikro/SN-Novelty-Brain-Comm.

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

  • Funding: added Deutsche Forschungsgemeinschaft: 425899996; Deutsches Zentrum für Neurodegenerative Erkrankungen: BN012; Otto von Guericke University Magdeburg

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 26 authors, 5 keywords, 88 references.

Cite

This paper

Krohn, F., Sarkar, M., Schütze, H., Iliopoulos, P., Penalba-Sánchez, L., Hämmerer, D., Yakupov, R., Lüsebrink, F., Spottke, A., Schneider, A., Roy, N., Incesoy, E., Heneka, M., Kilimann, I., Kleineidam, L., Teipel, S. J., Brosseron, F., Goerss, D., Glanz, W., . . . Betts, M. J. (2026). Substantia Nigra MRI markers are lower in Alzheimer's disease and are linked to general cognitive function. Brain communications, 8(4), fcag238. https://doi.org/10.1093/braincomms/fcag238

BibTeX

@article{krohn2026substantia,
author = {Krohn, Friedrich and Sarkar, Mousumi and Schütze, Hartmut and Iliopoulos, Panagiotis and Penalba-Sánchez, Lucía and Hämmerer, Dorothea and Yakupov, Renat and Lüsebrink, Falk and Spottke, Annika and Schneider, Anja and Roy, Nina and Incesoy, Enise and Heneka, Michael and Kilimann, Ingo and Kleineidam, Luca and Teipel, Stefan J and Brosseron, Frederic and Goerss, Doreen and Glanz, Wenzel and Schmid, Matthias and Rostamzadeh, Ayda and Wagner, Michael and Fliessbach, Klaus and Jessen, Frank Olaf and Düzel, Emrah and Betts, Matthew J},
title = {{Substantia Nigra MRI markers are lower in Alzheimer's disease and are linked to general cognitive function}},
journal = {Brain communications},
year = {2026},
month = jun,
volume = {8},
number = {4},
pages = {fcag238},
publisher = {Oxford University Press},
issn = {2632-1297},
doi = {10.1093/braincomms/fcag238},
url = {https://doi.org/10.1093/braincomms/fcag238},
pmid = {42488758},
pmcid = {PMC13390642}
}

RIS

TY - JOUR
AU - Krohn, Friedrich
AU - Sarkar, Mousumi
AU - Schütze, Hartmut
AU - Iliopoulos, Panagiotis
AU - Penalba-Sánchez, Lucía
AU - Hämmerer, Dorothea
AU - Yakupov, Renat
AU - Lüsebrink, Falk
AU - Spottke, Annika
AU - Schneider, Anja
AU - Roy, Nina
AU - Incesoy, Enise
AU - Heneka, Michael
AU - Kilimann, Ingo
AU - Kleineidam, Luca
AU - Teipel, Stefan J
AU - Brosseron, Frederic
AU - Goerss, Doreen
AU - Glanz, Wenzel
AU - Schmid, Matthias
AU - Rostamzadeh, Ayda
AU - Wagner, Michael
AU - Fliessbach, Klaus
AU - Jessen, Frank Olaf
AU - Düzel, Emrah
AU - Betts, Matthew J
TI - Substantia Nigra MRI markers are lower in Alzheimer's disease and are linked to general cognitive function
T2 - Brain communications
J2 - Brain Commun
PY - 2026
DA - 2026/06/24
VL - 8
IS - 4
SP - fcag238
SN - 2632-1297
PB - Oxford University Press
DO - 10.1093/braincomms/fcag238
UR - https://doi.org/10.1093/braincomms/fcag238
LA - en
ER -

CSL-JSON

{
"id": "10.1093/braincomms/fcag238",
"type": "article-journal",
"title": "Substantia Nigra MRI markers are lower in Alzheimer's disease and are linked to general cognitive function",
"container-title": "Brain communications",
"author": [
{
"family": "Krohn",
"given": "Friedrich"
},
{
"family": "Sarkar",
"given": "Mousumi"
},
{
"family": "Schütze",
"given": "Hartmut"
},
{
"family": "Iliopoulos",
"given": "Panagiotis"
},
{
"family": "Penalba-Sánchez",
"given": "Lucía"
},
{
"family": "Hämmerer",
"given": "Dorothea"
},
{
"family": "Yakupov",
"given": "Renat"
},
{
"family": "Lüsebrink",
"given": "Falk"
},
{
"family": "Spottke",
"given": "Annika"
},
{
"family": "Schneider",
"given": "Anja"
},
{
"family": "Roy",
"given": "Nina"
},
{
"family": "Incesoy",
"given": "Enise"
},
{
"family": "Heneka",
"given": "Michael"
},
{
"family": "Kilimann",
"given": "Ingo"
},
{
"family": "Kleineidam",
"given": "Luca"
},
{
"family": "Teipel",
"given": "Stefan J"
},
{
"family": "Brosseron",
"given": "Frederic"
},
{
"family": "Goerss",
"given": "Doreen"
},
{
"family": "Glanz",
"given": "Wenzel"
},
{
"family": "Schmid",
"given": "Matthias"
},
{
"family": "Rostamzadeh",
"given": "Ayda"
},
{
"family": "Wagner",
"given": "Michael"
},
{
"family": "Fliessbach",
"given": "Klaus"
},
{
"family": "Jessen",
"given": "Frank Olaf"
},
{
"family": "Düzel",
"given": "Emrah"
},
{
"family": "Betts",
"given": "Matthew J"
}
],
"container-title-short": "Brain Commun",
"volume": "8",
"issue": "4",
"page": "fcag238",
"DOI": "10.1093/braincomms/fcag238",
"PMID": "42488758",
"PMCID": "PMC13390642",
"ISSN": "2632-1297",
"publisher": "Oxford University Press",
"URL": "https://doi.org/10.1093/braincomms/fcag238",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
24
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1038/s41467-026-71831-z [code]
Dysfunction of the episodic memory network in the Alzheimer's disease cascade.
Journal: Nature communications
In common: SPM, Statistics and Machine Learning Toolbox, pandas, Alzheimer's / dementia, cognitive, 5 references, 2 authors
[2] doi:10.1016/j.nicl.2026.104039 [code]
The quest for the best: manual, atlas- and spatial prior-based delineation of locus coeruleus.
Journal: NeuroImage. Clinical
In common: structural MRI / diffusion, 5 references
[3] doi:10.1162/imag.a.1208 [code]
Brain network analysis in Alzheimer's disease and mild cognitive impairment using high-density diffuse optical tomography.
Journal: Imaging neuroscience (Cambridge, Mass.)
In common: SPM, statsmodels, Statistics and Machine Learning Toolbox, 1 other tool, Alzheimer's / dementia, 3 references
[4] doi:10.1002/ana.78227
Alzheimer's Disease Co-Pathology and Cognitive Impairment in Amyotrophic Lateral Sclerosis.
Journal: Annals of neurology
In common: Alzheimer's / dementia, 2 references, author Emrah Düzel
[5] doi:10.1186/s13195-026-02054-z [code]
Pathways to resilience: relationships between cognitive reserve, psychological debt, and Alzheimer's disease biomarkers.
Journal: Alzheimer's research & therapy
In common: Alzheimer's / dementia, 2 references, author Emrah Düzel
[6] doi:10.1038/s41386-026-02426-x [code]
A frontotemporal dementia-like phenotype in schizophrenia: links to striatal dopamine and iron accumulation.
Journal: Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology
In common: SPM, Statistics and Machine Learning Toolbox, pandas, Alzheimer's / dementia, structural MRI / diffusion, 3 references
[7] doi:10.1038/s41467-026-74957-2 [code]
Joint trajectories of brain atrophy, white matter hyperintensities and cognition quantify brain maintenance.
Journal: Nature communications
In common: Alzheimer's / dementia, cognitive, structural MRI / diffusion, 1 reference, author Renat Yakupov
[8] doi:10.1038/s42003-026-10276-y [code]
The cellular correlates and adolescent reorganisation of cortical myelination networks in the common marmoset.
Journal: Communications biology
In common: Pingouin, SPM, statsmodels, 2 other tools, structural MRI / diffusion, 1 reference
[9] doi:10.7554/elife.108408 [code]
Frequency and laminar profile of feature-specific visual activity revealed by interleaved EEG-fMRI.
Journal: eLife
In common: Pingouin, SPM, statsmodels, 2 other tools, 1 reference
[10] doi:10.1002/alz.71365 [code]
Benchmarking speech biomarkers of Alzheimer's against cognitive and neural measures.
Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association
In common: Pingouin, statsmodels, pandas, Alzheimer's / dementia, cognitive, 2 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.