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Postmortem brain MRI reveals differential associations of subcortical and limbic volumes with cortical thinning and neurodegenerative pathologies.

Code ↔ Paper

11 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 11 matches
  1. [1] § RESULTS › AD, FTLD‐TDP, and FTLD‐tau have lower subcortical and limbic volumes than LBD ↔ subcortical_analyses.ipynb, lines 111–128 · score 0.69 · Lewy body disease, likelihood ratio, ICV normalized postmortem, subcortical volumes, Pairwise, FTLD TDP
  2. [2] § RESULTS › Subcortical and limbic volume loss tracks with cortical thinning differently in each disease ↔ subcortical_cortical_analyses.ipynb, lines 169–176 · score 0.68 · partial Spearman correlations, normalized weighted, ICV normalized, cortical thickness, composite, coefficients
  3. [3] § RESULTS › AD, FTLD‐TDP, and FTLD‐tau have lower subcortical and limbic volumes than LBD ↔ subcortical_cortical_analyses.ipynb, lines 410–432 · score 0.66 · Boxplots compare, Lewy body disease, likelihood ratio, FTLD tau, Pairwise, FTLD TDP
  4. [4] § RESULTS › Polypathological models suggest primary pathology mostly drives subcortical and limbic volume loss ↔ subcortical_analyses.ipynb, lines 2632–2637 · score 0.65 · standardized coefficients, pathology predictors, OLS models, FDR correction, fitting, covariates
  5. [5] § METHODS › Semi‐quantitative neuropathology and histology measures ↔ notebooks/analysis_notebook_10_5_23.ipynb, lines 428–523 · score 0.60 · angular gyrus, cingulate, superior, temporal, field, frontal
  6. [6] § METHODS › Semi‐quantitative neuropathology and histology measures ↔ subcortical_analyses.ipynb, lines 23–54 · score 0.59 · Semi quantitative, antibodies, pons, brainstem, neurons, scores
  7. [7] § METHODS › Statistical analysis › Structural group differences and subcortical–cortical associations ↔ subcortical_cortical_analyses.ipynb, lines 328–407 · score 0.59 · DKT atlas, partial Spearman, cortical region, nucleus, thickness, correlations
  8. [8] § RESULTS › Primary AD is linked to worse subcortical and cortical atrophy than primary LBD in donors with both AD and LBD copathologies ↔ subcortical_analyses.ipynb, lines 1248–1288 · score 0.55 · normalized postmortem subcortical, Pathology burden, Primary pathology, linear, fit, age
  9. [9] § RESULTS › Histologic neuronal loss and gliosis mediate relationships between subcortical and limbic pathology and volume loss ↔ subcortical_analyses.ipynb, lines 545–562 · score 0.53 · regional pathology burden, FDR correction, postmortem subcortical, age, sex, education
  10. [10] § RESULTS › Polypathological models suggest primary pathology mostly drives subcortical and limbic volume loss ↔ subcortical_analyses.ipynb, lines 3070–3218 · score 0.52 · polypathology model, multiple pathologies, FTLD TDP, synuclein, tauopathy, regression
  11. [11] § RESULTS › Primary AD is linked to worse subcortical and cortical atrophy than primary LBD in donors with both AD and LBD copathologies ↔ notebooks/analysis_notebook_10_5_23.ipynb, lines 428–523 · score 0.51 · superior parietal, globus pallidus, cortex, thicknesses, caudate, cortical

Paper

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The authors' code

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Overview

Authors: Pulkit Khandelwal1,2, Michael Tran Duong1, Lisa M Levorse1, Winifred Trotman1, Alejandra Bahena1, Sydney A Lim1, Amanda E Denning1, Eunice Chung1, Christopher A Olm1, Hamsanandini Radhakrishnan1, Ranjit Ittyerah1, Karthik Prabhakaran1, Gabor Mizsei1, Theresa Schuck1, Sheina Emrani1, Joaquin A Vizcarra1, John Robinson1, Daniel T Ohm1, Jeffrey S Phillips1, Jesse Cohen3
and 11 other authorsLaura E M Wisse4, John A Detre1, Ilya M Nasrallah1, Christopher A Brown1, Sandhitsu R Das1, Edward B Lee1, M Dylan Tisdall1, David J Irwin1, Corey T McMillan1, David A Wolk1, Paul A Yushkevich1
ORCID iDs: Michael Tran Duong
  1. University of Pennsylvania, Philadelphia, Pennsylvania, USA
  2. Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
  3. University of Florida, Jacksonville, Florida, USA
  4. Lund University, Lund, Sweden
Institutions: Harvard University (United States); Massachusetts General Hospital (United States); Athinoula A. Martinos Center for Biomedical Imaging (United States); University of Pennsylvania (United States); University of Florida (United States); Lund University (Sweden)
Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association, volume 22, issue 7, article e71649
Dates: received 7 January 2026; accepted 6 June 2026; published online 8 July 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1002/alz.71649 · PMID 42418450 · PMCID PMC13344898 · OpenAlex W7167693549
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), histology / microscopy (modality), human (organism), other condition (population), Alzheimer's / dementia (population), Parkinson's (population), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Connectivity, Preprocessing
Keywords: ADRD, alzheimer's disease, alzheimer's disease and related dementias, copathologies, entorhinal cortex, ex vivo magnetic resonance imaging (MRI), frontotemporal lobar degeneration with transactive response DNA binding protein 43 (FTLD‐TDP), FTLD‐tau, lewy body dementia, neuroimaging, neuropathologies, postmortem imaging, subcortical structures, synuclein, tau, TDP‐43
MeSH: Alzheimer Disease*, Brain*, Cerebral Cortical Thinning*, Frontotemporal Lobar Degeneration*, Lewy Body Disease*, Limbic System*, Magnetic Resonance Imaging*, Neurodegenerative Diseases*, Aged, Aged, 80 and over, alpha-Synuclein, Atrophy, DNA-Binding Proteins, Female, Humans, Male, Middle Aged, tau Proteins (* major topic)
Topic: Dementia and Cognitive Impairment Research (Psychiatry and Mental health, Medicine), according to OpenAlex
Funding: NIH HHS (P01 AG017586, F30 AG074524, P30 AG072979, U19 AG062418, P01 AG066597, R01 NS109260, RF1 AG056014, P01 AG084497, R01 AG054519, R01 AG069474); National Institutes of Health (R01 AG054519, P01 AG084497, U19 AG062418, P01 AG017586, P01 AG066597, R01 NS109260, F30 AG074524, P30 AG072979, R01 AG069474, RF1 AG056014)
Citations: not cited yet (Europe PMC); 74 references in the paper

Abstract

INTRODUCTION: The impact of different neuropathologies on deep brain structures remains to be understood. We examine subcortical and limbic volumetry in neurodegenerative diseases involving phosphorylated tau (p‐tau), α‐synuclein, and transactive response DNA binding protein 43 (TDP‐43).

METHODS: We acquired neuropathological measures and brain segmentations from postmortem analysis of 132 donors with Alzheimer's disease (AD), Lewy body disease (LBD), frontotemporal lobar degeneration with TDP‐43 (FTLD‐TDP), and FTLD‐tau.

RESULTS: LBD had the least subcortical, limbic, and cortical atrophy compared to AD, FTLD‐TDP, and FTLD‐tau. In donors with both AD and LBD pathologies, primary LBD was associated with less atrophy than primary AD. While AD had cortico‐subcortical and cortico‐limbic morphometric associations, LBD had more limited parieto‐occipital cortico‐limbic associations. FTLD‐TDP had cortico‐subcortical while FTLD‐tau had cortico‐subcortical and cortico‐limbic associations. In AD and FTLD‐tau, hippocampal volumes correlated with p‐tau burden, neuron loss, and gliosis. In LBD, thalamic α‐synuclein severity was associated with subcortical/limbic volumes.

DISCUSSION: Postmortem neuroimaging reveals disease‐ and region‐specific structure–pathology relationships.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 11 matches between paragraphs and lines of code.

Pulkit-Khandelwal/purple-mri

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 671f35b6d8eb41e3f75c4ff3b16cedc1986a9b24, 10 September 2026
Languages: Shell (39), Python (29), C++ (1), Jupyter (1)
Size: 178 files, 70 scripts
Software Heritage: not archived
Found in: the text, “Image analysis”
Holds: README, environment (pyproject.toml, docs/requirements.txt, pkg_src/pyproject.toml, docker/nighres_docker/Dockerfile, docker/segmentation_docker/Dockerfile, docker/segmentation_docker/requirements.txt, docs/source/_static/singularity.png), documentation, 1 notebook
Not found: license file, CITATION.cff, tests, continuous integration
Tools: NumPy (24 files), FreeSurfer (21 files), PyTorch (14 files), SciPy (13 files), SimpleITK (12 files), nnU-Net (11 files), OpenCV (9 files), pandas (7 files), NiBabel (6 files), ANTs (2 files), Matplotlib (2 files), Pillow (2 files), FSL (1 file), Nighres (1 file), Pingouin (1 file), Plotly (1 file), scikit-image (1 file), scikit-learn (1 file), seaborn (1 file), statannotations (1 file), statsmodels (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
71 files, not copied: shown from their source

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At the source: github.com/Pulkit-Khandelwal/purple-mri

Pulkit-Khandelwal/postmortem-subcortical-limbic-pathologies

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 6abfd1d98fa06009578e0e292a72996ba3e46a58, 5 May 2026
Languages: Jupyter (2)
Size: 3 files, 2 scripts
Software Heritage: not archived
Found in: the text, “Statistical analysis”
Holds: README, 2 notebooks
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Matplotlib (2 files), NumPy (2 files), pandas (2 files), Pingouin (2 files), SciPy (2 files), seaborn (2 files), statsmodels (2 files), NiBabel (1 file), Pillow (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
3 files, not copied: shown from their source

OSCR keeps no copy of these files: this repository has no license that allows it. The reader above shows each one from its source, fetched by your browser at commit 6abfd1d, when its fingerprint is the one OSCR verified. How this works.

At the source: github.com/Pulkit-Khandelwal/postmortem-subcortical-limbic-pathologies

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  • 72 scripts, each with its path and the digest of its content;
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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 31 authors, 16 keywords, 18 MeSH terms, 2 funders, 71 references.

Cite

This paper

Khandelwal, P., Duong, M. T., Levorse, L. M., Trotman, W., Bahena, A., Lim, S. A., Denning, A. E., Chung, E., Olm, C. A., Radhakrishnan, H., Ittyerah, R., Prabhakaran, K., Mizsei, G., Schuck, T., Emrani, S., Vizcarra, J. A., Robinson, J., Ohm, D. T., Phillips, J. S., . . . Yushkevich, P. A. (2026). Postmortem brain MRI reveals differential associations of subcortical and limbic volumes with cortical thinning and neurodegenerative pathologies. Alzheimer's & dementia : the journal of the Alzheimer's Association, 22(7), e71649. https://doi.org/10.1002/alz.71649

BibTeX

@article{khandelwal2026postmortem,
author = {Khandelwal, Pulkit and Duong, Michael Tran and Levorse, Lisa M and Trotman, Winifred and Bahena, Alejandra and Lim, Sydney A and Denning, Amanda E and Chung, Eunice and Olm, Christopher A and Radhakrishnan, Hamsanandini and Ittyerah, Ranjit and Prabhakaran, Karthik and Mizsei, Gabor and Schuck, Theresa and Emrani, Sheina and Vizcarra, Joaquin A and Robinson, John and Ohm, Daniel T and Phillips, Jeffrey S and Cohen, Jesse and Wisse, Laura E M and Detre, John A and Nasrallah, Ilya M and Brown, Christopher A and Das, Sandhitsu R and Lee, Edward B and Tisdall, M Dylan and Irwin, David J and McMillan, Corey T and Wolk, David A and Yushkevich, Paul A},
title = {{Postmortem brain MRI reveals differential associations of subcortical and limbic volumes with cortical thinning and neurodegenerative pathologies}},
journal = {Alzheimer's \& dementia : the journal of the Alzheimer's Association},
year = {2026},
month = jul,
volume = {22},
number = {7},
pages = {e71649},
publisher = {Wiley},
issn = {1552-5260},
doi = {10.1002/alz.71649},
url = {https://doi.org/10.1002/alz.71649},
pmid = {42418450},
pmcid = {PMC13344898}
}

RIS

TY - JOUR
AU - Khandelwal, Pulkit
AU - Duong, Michael Tran
AU - Levorse, Lisa M
AU - Trotman, Winifred
AU - Bahena, Alejandra
AU - Lim, Sydney A
AU - Denning, Amanda E
AU - Chung, Eunice
AU - Olm, Christopher A
AU - Radhakrishnan, Hamsanandini
AU - Ittyerah, Ranjit
AU - Prabhakaran, Karthik
AU - Mizsei, Gabor
AU - Schuck, Theresa
AU - Emrani, Sheina
AU - Vizcarra, Joaquin A
AU - Robinson, John
AU - Ohm, Daniel T
AU - Phillips, Jeffrey S
AU - Cohen, Jesse
AU - Wisse, Laura E M
AU - Detre, John A
AU - Nasrallah, Ilya M
AU - Brown, Christopher A
AU - Das, Sandhitsu R
AU - Lee, Edward B
AU - Tisdall, M Dylan
AU - Irwin, David J
AU - McMillan, Corey T
AU - Wolk, David A
AU - Yushkevich, Paul A
TI - Postmortem brain MRI reveals differential associations of subcortical and limbic volumes with cortical thinning and neurodegenerative pathologies
T2 - Alzheimer's & dementia : the journal of the Alzheimer's Association
J2 - Alzheimers Dement
PY - 2026
DA - 2026/07/01
VL - 22
IS - 7
SP - e71649
SN - 1552-5260
PB - Wiley
DO - 10.1002/alz.71649
UR - https://doi.org/10.1002/alz.71649
LA - en
ER -

CSL-JSON

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