Vulnerability of anterior medial temporal lobe subregions to early tau-related neurodegeneration in Alzheimer's disease: Converging evidence from tau-PET and plasma p-tau217.

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The authors' code

Python · 172 lines · 5 KB · GPL-3.0

# -*- coding: utf-8 -*-
#
# cmrep documentation build configuration file, created by
# sphinx-quickstart on Thu Nov 21 09:26:55 2019.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.mathjax',
'sphinx.ext.githubpages']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'cmrep'
copyright = u'2019, Paul A. Yushkevich'
author = u'Paul A. Yushkevich'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = u'1.0'
# The full version, including alpha/beta/rc tags.
release = u'1.0.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = []
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = False
# -- Options for HTML output ----------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx_rtd_theme'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#
# html_theme_options = {}
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# This is required for the alabaster theme
# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
html_sidebars = {
'**': [
'about.html',
'navigation.html',
'relations.html', # needs 'show_related': True theme option to display
'searchbox.html',
'donate.html',
]
}
# -- Options for HTMLHelp output ------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'cmrepdoc'
# -- Options for LaTeX output ---------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#
# 'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#
# 'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#
# 'preamble': '',
# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'cmrep.tex', u'cmrep Documentation',
u'Paul A. Yushkevich', 'manual'),
]
# -- Options for manual page output ---------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'cmrep', u'cmrep Documentation',
[author], 1)
]
# -- Options for Texinfo output -------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
(master_doc, 'cmrep', u'cmrep Documentation',
author, 'cmrep', 'One line description of project.',
'Miscellaneous'),
]

conf.py at commit c0760b4, under GPL-3.0 · at the source

Overview

Authors: Nidhi S Mundada¹, Niyousha Sadeghpour², Emily McGrew³, Hannah L Tucker⁴, Ilya M Nasrallah², Sandhitsu R Das³, David A Wolk³, Paul A Yushkevich², Christopher A Brown³, Laura E M Wisse⁴

ORCID iDs: Nidhi S Mundada

Institutions: University of Pennsylvania (United States); Lund University (Sweden)

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association, volume 22, issue 6, article e71571

Dates: received 28 January 2026; accepted 4 May 2026; published online 17 June 2026; in print June 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1002/alz.71571 · PMID 42309984 · PMCID PMC13275324 · OpenAlex W7165013860

Open access: hybrid, a free copy (OpenAlex)

Status: code verified

Categories: structural MRI / diffusion (modality), other (modality), PET / SPECT (modality), human (organism), other condition (population), Alzheimer's / dementia (population), cellular / molecular (subfield)

Methods: Connectivity, Statistics, fMRI & imaging, Preprocessing

Keywords: Brodmann area 35, medial temporal lobe, neurodegeneration, plasma phosphorylated tau 217 (p‐tau217), preclinical Alzheimer's disease, structural magnetic resonance imaging, tau pathology, tau positron emission tomography (PET)

MeSH: Alzheimer Disease*, tau Proteins*, Temporal Lobe*, Aged, Aged, 80 and over, Amyloid beta-Peptides, Female, Humans, Magnetic Resonance Imaging, Male, Phosphorylation, Positron-Emission Tomography (* major topic)

Topic: Alzheimer's disease research and treatments (Physiology, Medicine), according to OpenAlex

Funding: Alzheimerfonden (AF‐1010833, AF-1010833); NIA NIH HHS (R01 AG069474, R01-AG070952, R01 AG056014, P30 AG072979); National Institute on Aging (R01‐AG070952); National Science Foundation (R01‐AG072796, R01-AG072796); Greta and Johan Kockska Foundation; Multipark; Crafoordska Stiftelsen (20210690); Foundation for the National Institutes of Health (R01-AG056014, R01‐AG056014); Alzheimer’s Association (AACSF-23-1152241); Vetenskapsrådet (2022‐00900); Swedish Research Council (2022-00900); Alzheimer's Association (AACSF‐23‐1152241)

Citations: not cited yet (Europe PMC); 50 references in the paper

Abstract

INTRODUCTION: The anterior medial temporal lobe (MTL), including the entorhinal cortex (ERC) and Brodmann area 35 (BA35), is among the earliest cortical sites of tau pathology in Alzheimer's disease (AD), yet conventional image segmentation methods poorly capture these regions.

METHODS: We applied an automated segmentation approach using an extended Automatic Segmentation of Hippocampal Subfields (ASHS) atlas, including anterior MTL subregions, in 448 Pennsylvania Alzheimer's Disease Research Center participants with magnetic resonance imaging, tau positron emission tomography (PET) (n = 199), and/or plasma phosphorylated tau 217 (p‐tau217) (n = 377). Amyloid beta (Aβ) positivity was defined using PET or plasma.

RESULTS: Tau‐PET showed an anterior–posterior gradient, with highest uptake in BA35, ERC, and anterior hippocampus. Increased MTL tau‐PET uptake and plasma p‐tau217 were associated with cortical thinning localized to BA35 and ERC, even in cognitively unimpaired Aβ‐positive individuals.

CONCLUSIONS: Anterior MTL subregions, especially BA35, show early vulnerability to tau‐related neurodegeneration. Extended anterior MTL parcellation improves localization of early tau‐associated structural changes and may facilitate biological staging in preclinical AD.

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

Repository

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

pyushkevich/cmrep

License: GPL-3.0

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: c0760b45a8fcb1358619e46fc5c09b1f6e34e7b8, 3 February 2026

Languages: C/C++ (75), MATLAB (17), C (5), C++ (2), Python (1), Jupyter (1), Shell (1)

Size: 314 files, 102 scripts

Software Heritage: archived

Found in: the text, “Statistical analysis”

Holds: README, license file, environment (Dockerfile), documentation, 1 notebook

Not found: CITATION.cff, tests, continuous integration

Tools: Image Processing Toolbox (4 files), NumPy (1 file), PyTorch (1 file)

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

104 files

docs/source/conf.py, Python, 172 lines
extras/toms611/toms611.c, C, 6,769 lines
extras/triangle/showme.c, C, 3,375 lines
extras/triangle/triangle.c, C, 4,420 lines
extras/triangle/triangle.h, C/C++, 289 lines
extras/triangle/tricall.c, C, 273 lines
scripts/jupyter/quat.ipynb, Jupyter, 194 lines
scripts/matlab/experimental/options_caphg.m, MATLAB, 61 lines
scripts/matlab/experimental/options_cbrun_ifo.m, MATLAB, 66 lines
scripts/matlab/experimental/options_postleaf.m, MATLAB, 64 lines
scripts/matlab/experimental/sampcurv.m, MATLAB, 32 lines
scripts/matlab/experimental/tempinit_afront.m, MATLAB, 337 lines
scripts/matlab/experimental/tempinit_anterior_leaflet.m, MATLAB, 208 lines
scripts/matlab/experimental/tempinit_polyfit.m, MATLAB, 39 lines
scripts/matlab/experimental/tempinit_polyinterp.m, MATLAB, 20 lines
scripts/matlab/experimental/tempinit_posterior_leaflet.m, MATLAB, 208 lines
scripts/matlab/experimental/tempinit_sampcurv.m, MATLAB, 64 lines
scripts/matlab/experimental/tempinit_triangle.m, MATLAB, 42 lines
scripts/matlab/tempinit.m, MATLAB, 155 lines
scripts/matlab/vtk_add_point_data.m, MATLAB, 36 lines
scripts/matlab/vtk_get_point_data.m, MATLAB, 11 lines
scripts/matlab/vtk_polydata_read.m, MATLAB, 231 lines
scripts/matlab/vtk_polydata_write.m, MATLAB, 96 lines
src/AffineTransformDescriptor.h, C/C++, 303 lines
src/BasisFunctions2D.h, C/C++, 445 lines
src/BoundaryConstrainedCMRepObjectives.h, C/C++, 145 lines
src/BranchingSubdivisionSurface.h, C/C++, 525 lines
src/BruteForceSubdivisionMedialModel.h, C/C++, 135 lines
src/CartesianGridMedialIterationContext.h, C/C++, 144 lines
src/CartesianMedialAtomGrid.h, C/C++, 78 lines
src/CartesianMedialModel.h, C/C++, 234 lines
src/CoarseToFineMappingDescriptor.h, C/C++, 173 lines
src/CodeTimer.h, C/C++, 34 lines
src/CoefficientMapping.h, C/C++, 447 lines
src/CoefficientMask.h, C/C++, 292 lines
src/DiffeomorphicEnergyTerm.h, C/C++, 86 lines
src/EigenSolverInterface.h, C/C++, 61 lines
src/FastLinearInterpolator.h, C/C++, 901 lines
src/GenericMedialModel.h, C/C++, 236 lines
src/GentleNLP.h, C/C++, 962 lines
src/GeometryDescriptor.h, C/C++, 38 lines
src/IPOptProblemInterface.h, C/C++, 73 lines
src/IPOptQCQPProblemInterface.h, C/C++, 73 lines
src/ITKImageWrapper.h, C/C++, 63 lines
src/JacobianDistortionPenaltyTerm.h, C/C++, 138 lines
src/MKLSolverInterface.h, C/C++, 72 lines
src/MedialAtom.h, C/C++, 180 lines
src/MedialAtomGrid.h, C/C++, 457 lines
src/MedialAtomIterators.h, C/C++, 403 lines
src/MedialException.h, C/C++, 20 lines
src/MedialIterationContext.h, C/C++, 96 lines
src/MedialModelIO.h, C/C++, 33 lines
src/MedialPDEMasks.h, C/C++, 249 lines
src/MedialPDERenderer.h, C/C++, 28 lines
src/MedialPDESites.h, C/C++, 186 lines
src/MedialPDESolver.h, C/C++, 178 lines
src/MeshMedialPDESolver.h, C/C++, 190 lines
src/MeshTraversal.h, C/C++, 452 lines
src/NonparametricSubdivisionMedialModel.h, C/C++, 1 line
src/OptimizationParameters.h, C/C++, 113 lines
src/OptimizationTerms.h, C/C++, 1,552 lines
src/PDESubdivisionMedialModel.h, C/C++, 98 lines
src/ParameterFile.h, C/C++, 5 lines
src/PardisoInterface.h, C/C++, 114 lines
src/PointSetOptimalControlSystem.h, C/C++, 127 lines
src/PrincipalComponents.h, C/C++, 102 lines
src/PrincipalComponentsPenaltyTerm.h, C/C++, 46 lines
src/Procrustes.h, C/C++, 20 lines
src/QCQPProblem.h, C/C++, 828 lines
src/Registry.h, C/C++, 339 lines
src/ScriptInterface.h, C/C++, 493 lines
src/SmoothedImageSampler.h, C/C++, 77 lines
src/SparseMatrix.h, C/C++, 290 lines
src/SparseSolver.h, C/C++, 45 lines
src/SubdivisionMedialModel.h, C/C++, 151 lines
src/SubdivisionSurface.h, C/C++, 116 lines
src/SubdivisionSurfaceMedialIterationContext.h, C/C++, 91 lines
src/System.h, C/C++, 6 lines
src/TaucsInterface.h, C/C++, 68 lines
src/TestSolver.h, C/C++, 32 lines
src/VTKMeshBuilder.h, C/C++, 67 lines
src/ctpl_stl.h, C/C++, 251 lines
src/dijkstra/BinaryHeap.h, C/C++, 274 lines
src/dijkstra/ShortestPath.h, C/C++, 266 lines
src/dijkstra/VTKMeshHalfEdgeWrapper.h, C/C++, 220 lines
src/dijkstra/VTKMeshShortestDistance.h, C/C++, 245 lines
src/exp_approx.h, C/C++, 54 lines
src/itkOrientedRASImage.h, C/C++, 193 lines
src/itk_to_nifti_xform.h, C/C++, 58 lines
src/smlmath.h, C/C++, 93 lines
src/util/DrawFillInside.cpp, C++, 92 lines
src/util/DrawFillInside.h, C/C++, 14 lines
src/util/DrawTriangles.cpp, C++, 698 lines
src/util/DrawTriangles.h, C/C++, 74 lines
src/util/ReadWriteVTK.h, C/C++, 16 lines
src/util/TetraLib.h, C/C++, 11 lines
src/util/VCGTriMesh.h, C/C++, 61 lines
src/util/VTKArrays.h, C/C++, 61 lines
src/util/asa243.c, C, 960 lines
src/util/asa243.h, C/C++, 8 lines
testing/bcmrep/placenta_fit.sh, Shell, 30 lines
testing/meshglm/generate_test.m, MATLAB, 91 lines
COPYING, License, 674 lines
README.md, Text, 17 lines

At the source: github.com/pyushkevich/cmrep

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.

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102 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, 10 authors, 8 keywords, 12 MeSH terms, 12 funders, 50 references.

Cite

This paper

Mundada, N. S., Sadeghpour, N., McGrew, E., Tucker, H. L., Nasrallah, I. M., Das, S. R., Wolk, D. A., Yushkevich, P. A., Brown, C. A., & Wisse, L. E. M. (2026). Vulnerability of anterior medial temporal lobe subregions to early tau-related neurodegeneration in Alzheimer's disease: Converging evidence from tau-PET and plasma p-tau217. Alzheimer's & dementia : the journal of the Alzheimer's Association, 22(6), e71571. https://doi.org/10.1002/alz.71571

BibTeX

@article{mundada2026vulnerability, author = {Mundada, Nidhi S and Sadeghpour, Niyousha and McGrew, Emily and Tucker, Hannah L and Nasrallah, Ilya M and Das, Sandhitsu R and Wolk, David A and Yushkevich, Paul A and Brown, Christopher A and Wisse, Laura E M}, title = {{Vulnerability of anterior medial temporal lobe subregions to early tau-related neurodegeneration in Alzheimer's disease: Converging evidence from tau-PET and plasma p-tau217}}, journal = {Alzheimer's \& dementia : the journal of the Alzheimer's Association}, year = {2026}, month = jun, volume = {22}, number = {6}, pages = {e71571}, publisher = {Wiley}, issn = {1552-5260}, doi = {10.1002/alz.71571}, url = {https://doi.org/10.1002/alz.71571}, pmid = {42309984}, pmcid = {PMC13275324} }

RIS

TY - JOUR AU - Mundada, Nidhi S AU - Sadeghpour, Niyousha AU - McGrew, Emily AU - Tucker, Hannah L AU - Nasrallah, Ilya M AU - Das, Sandhitsu R AU - Wolk, David A AU - Yushkevich, Paul A AU - Brown, Christopher A AU - Wisse, Laura E M TI - Vulnerability of anterior medial temporal lobe subregions to early tau-related neurodegeneration in Alzheimer's disease: Converging evidence from tau-PET and plasma p-tau217 T2 - Alzheimer's & dementia : the journal of the Alzheimer's Association J2 - Alzheimers Dement PY - 2026 DA - 2026/06/01 VL - 22 IS - 6 SP - e71571 SN - 1552-5260 PB - Wiley DO - 10.1002/alz.71571 UR - https://doi.org/10.1002/alz.71571 LA - en ER -

CSL-JSON

{ "id": "10.1002/alz.71571", "type": "article-journal", "title": "Vulnerability of anterior medial temporal lobe subregions to early tau-related neurodegeneration in Alzheimer's disease: Converging evidence from tau-PET and plasma p-tau217", "container-title": "Alzheimer's & dementia : the journal of the Alzheimer's Association", "author": [ { "family": "Mundada", "given": "Nidhi S" }, { "family": "Sadeghpour", "given": "Niyousha" }, { "family": "McGrew", "given": "Emily" }, { "family": "Tucker", "given": "Hannah L" }, { "family": "Nasrallah", "given": "Ilya M" }, { "family": "Das", "given": "Sandhitsu R" }, { "family": "Wolk", "given": "David A" }, { "family": "Yushkevich", "given": "Paul A" }, { "family": "Brown", "given": "Christopher A" }, { "family": "Wisse", "given": "Laura E M" } ], "container-title-short": "Alzheimers Dement", "volume": "22", "issue": "6", "page": "e71571", "DOI": "10.1002/alz.71571", "PMID": "42309984", "PMCID": "PMC13275324", "ISSN": "1552-5260", "publisher": "Wiley", "URL": "https://doi.org/10.1002/alz.71571", "language": "en", "issued": { "date-parts": [ [ 2026, 6, 1 ] ] } }

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