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Striosome-Like Structural Connectivity Is Reduced in the Rostral Putamen in Anxiety Disorder.

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 · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
  1. [1] § 2. Methods › 2.5. Striatal Parcellation With Classification Targets Tractography (CTT) ↔ DTI_CT_LC.StrioVsMat.extracts_MaskVolume.1.5SD.HCP.sh, the whole file · a weak match · score 0.56 · matrix volume, striosome volume, DTI, tractography, parcellations, hemisphere
  2. [2] § 2. Methods › 2.5. Striatal Parcellation With Classification Targets Tractography (CTT) ↔ DTI_StriosomeVsMatrix_MatchesMatrixToSmallStriosomeMasks_1.5SD.HCP.sh, lines 1–36 · score 0.55 · standard deviations, striatal voxel, uppermost, match, parcellations, waugh

Paper

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

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The authors' code

Shell · 46 lines · 1.7 KB · no license · 1 match

  1. #!/bin/bash
  2. #
  3. # This script extracts the volume of striatal masks derived from striosome/matrix parcellation.
  4. # For subsequent tractography to be meaningful, the mask volume for striosome-like and matrix-like
  5. # masks has to be equal.
  6. #
  7. #
  9. module unload fsl
  10. module load fsl/5.0.11
  12. experimental_directory=/project/pediatrics/Waugh_lab/shared/HCP
  13. cd ${experimental_directory}
  14. rm DTI_CT_StrioVsMat.MaskVolumes.txt
  15. echo -e "Group \t Hemisphere \t Identifier \t Matrix-like Volume, 1.5SD \t Striosome-like Volume, 1.5SD" > $experimental_directory/DTI_CT_StrioVsMat.MaskVolumes.txt
  17. segmented_region=trStriatum
  19. group=2018.N-1.E2
  21. for identifier in $(awk '{print $2}' HCP_peds.txt)
  22. do
  23. cd ${experimental_directory}
  25. DTI_directory=${identifier}/${identifier}_Diffusion
  26. cd ${experimental_directory}/${DTI_directory}.bedpostX
  27. rm temp_group temp_hemisphere temp_ID temp_Matrix_vol temp_Striosome_vol
  28. echo $directory
  29. echo "${group} " > temp_group
  30. echo "${identifier} " > temp_ID
  31. for hemisphere1 in Left Right
  32. do
  33. echo "${hemisphere1} " > temp_hemisphere
  34. echo "testing ${hemisphere1} hemisphere"
  35. for region1 in Striosome Matrix
  36. do
  37. fslstats ${identifier}_CT_LC_${hemisphere1}-${segmented_region}_to_${region1}-like_Ctx_${group}_excludesMidline_PT1_1.5SDthresh.nii.gz -V | awk '{print $1}' > temp_${region1}_vol
  38. done
  39. echo "pasting now"
  41. paste temp_group temp_hemisphere temp_ID temp_Matrix_vol temp_Striosome_vol >> ${experimental_directory}/DTI_CT_StrioVsMat.MaskVolumes.txt
  42. done
  43. rm temp_group temp_hemisphere temp_ID temp_Matrix_vol temp_Striosome_vol
  44. done
  45. cat ${experimental_directory}/DTI_CT_StrioVsMat.MaskVolumes.txt

DTI_CT_LC.StrioVsMat.extracts_MaskVolume.1.5SD.HCP.sh at commit 9817024, no license · at the source

Overview

Authors: Adrian T Funk1, Jeff L Waugh1,2
ORCID iDs: Adrian T Funk, Jeff L Waugh
  1. Division of Pediatric Neurology, University of Texas Southwestern, Dallas, Texas, USA, utsouthwestern.edu
  2. Department of Pediatrics and Department of Neurology, University of Texas Southwestern, Dallas, Texas, USA, utsouthwestern.edu
Institutions: The University of Texas Southwestern Medical Center (United States)
Journal: Depression and anxiety, volume 2026, issue 1, article 7682055
Dates: received 13 January 2025; accepted 10 March 2026; published online 8 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1155/da/7682055 · PMID 41971224 · PMCID PMC13062657 · OpenAlex W7152676003
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), human (organism), other condition (population), developmental (subfield)
Methods: Statistics, fMRI & imaging
Keywords: anxiety, compartment, matrix, striatum, striosome
MeSH: Anxiety Disorders*, Putamen*, Adolescent, Diffusion Tensor Imaging, Female, Humans, Male, Neural Pathways, Young Adult (* major topic)
Topic: Functional Brain Connectivity Studies (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: NINDS NIH HHS (K23 NS124978)
Citations: cited by 2 papers (Europe PMC); 67 references in the paper

Abstract

Anxiety disorders affect roughly a third of adults, and treatment of anxiety‐related symptoms costs more than any other mental health condition. Symptoms often begin in adolescence and are usually lifelong. Identifying shared neuroanatomical features of anxiety is essential for understanding its causes and improving treatments. Developmental abnormalities in the striatum, an obligate node in cortico–striato–thalamo–cortical networks, could predispose to the diverse symptoms of anxiety. The striatum is comprised of two interdigitated tissue compartments, striosome and matrix, that have different embryologic origins, divergent afferent/efferent connectivity, opposing responses to dopamine, and are embedded in distinct structural and functional networks. We used quantitative diffusion tractography to perform connectivity‐based parcellation, identifying striosome‐like and matrix‐like striatal voxels in a 295‐subject cohort (youth‐onset anxiety vs. matched controls). In anxiety, striosome‐like connectivity was depleted and dispersed, especially in a bilateral zone in the rostral putamen. Striosome‐like connectivity was inversely correlated with standardized assessments of anxiety. Matrix‐favoring connectivity was increased in a broad swath of cortico‐striate projections. Increases in the striatal matrix:striosome ratio may predispose individuals to anxiety.

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.

jeff-waugh/Striatal-Connectivity-based-Parcellation

License: none: the authors keep all their rights
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 9817024ae6fe8b69e18efb17dc26cea8b6a8d301, 29 May 2025
Languages: Shell (16)
Size: 48 files, 16 scripts
Software Heritage: not archived
Found in: the text, “2.5. Striatal Parcellation With Classification T”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: FSL (16 files), FreeSurfer (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
17 files
At the source: github.com/jeff-waugh/Striatal-Connectivity-based-Parcellation

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;
  • 16 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

Publicly available datasets were analyzed in this study. NDA data can be accessed at nda.nih.gov. The code, bait, seed, and exclusion masks necessary to complete striatal parcellation can be accessed here github.com/jeff-waugh/Striatal-Connectivity-based-Parcellation.

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, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 2 authors, 5 keywords, 9 MeSH terms, 1 funder, 67 references.

Cite

This paper

Funk, A. T., & Waugh, J. L. (2026). Striosome-Like Structural Connectivity Is Reduced in the Rostral Putamen in Anxiety Disorder. Depression and anxiety, 2026(1), 7682055. https://doi.org/10.1155/da/7682055

BibTeX

@article{funk2026striosome,
author = {Funk, Adrian T and Waugh, Jeff L},
title = {{Striosome-Like Structural Connectivity Is Reduced in the Rostral Putamen in Anxiety Disorder}},
journal = {Depression and anxiety},
year = {2026},
month = apr,
volume = {2026},
number = {1},
pages = {7682055},
publisher = {Wiley},
issn = {1091-4269},
doi = {10.1155/da/7682055},
url = {https://doi.org/10.1155/da/7682055},
pmid = {41971224},
pmcid = {PMC13062657}
}

RIS

TY - JOUR
AU - Funk, Adrian T
AU - Waugh, Jeff L
TI - Striosome-Like Structural Connectivity Is Reduced in the Rostral Putamen in Anxiety Disorder
T2 - Depression and anxiety
J2 - Depress Anxiety
PY - 2026
DA - 2026/04/08
VL - 2026
IS - 1
SP - 7682055
SN - 1091-4269
PB - Wiley
DO - 10.1155/da/7682055
UR - https://doi.org/10.1155/da/7682055
LA - en
ER -

CSL-JSON

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"PMID": "41971224",
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