OSCR

Morphological and anatomical variations in subcortical anatomy between humans and chimpanzees associated with heritability patterns related to human behavioral traits.

Code ↔ Paper

5 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 5 matches
  1. [1] § Materials and methods › Interspecies analysis: vertex-wise shape differences between humans and chimpanzees ↔ src/object_volume_dot_product.c, lines 1–10 · score 0.74 · volume dot product, deformation vector, surface normals
  2. [2] § Materials and methods › Intraspecies analysis: partial least squares correlation (PLSC) analysis in the Human Connectome Project (HCP) sampleσ ↔ pyls/types/behavioral.py, lines 245–294 · score 0.72 · linear combination, covariance matrix, brain features, covaries, singular, Pyls
  3. [3] § Materials and methods › Intraspecies analysis: partial least squares correlation (PLSC) analysis in the Human Connectome Project (HCP) sampleσ ↔ pyls/base.py, lines 438–527 · score 0.70 · bootstrap ratio, standard error, bootstrap resampling, SVD, singular, matrix
  4. [4] § Materials and methods › Intraspecies analysis: partial least squares correlation (PLSC) analysis in the Human Connectome Project (HCP) sampleσ ↔ pyls/types/regression.py, lines 56–186 · score 0.64 · linear combination, covariance matrix, residualized, algorithm, Squares, scored
  5. [5] § Materials and methods › Intraspecies analysis: partial least squares correlation (PLSC) analysis in the Human Connectome Project (HCP) sampleσ ↔ pyls/structures.py, lines 1–60 · score 0.54 · bootstrap resampling, reliability, SVD, singular, permutation, LV

Paper

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

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The authors' code

C · 87 lines · 2.6 KB · BSD-3-Clause · 1 match

  1. /* takes the dot product between a length of 3 deformation vector in a
  2. 4D volume and the surface normals of a polyhedral object.
  4. Author: Jason Lerch <[email hidden]>
  5. */
  6. #define HAVE_MINC2 1
  8. #include <volume_io.h>
  9. #include <bicpl.h>
  10. #include <stdio.h>
  12. int main(int argc, char *argv[]) {
  13. VIO_Volume grid_volume;
  14. VIO_File_formats format;
  15. VIO_Real dot_product, interp_values[3];
  16. object_struct **objects;
  17. int n_objects, sizes[VIO_MAX_DIMENSIONS], n_points, i;
  18. VIO_Vector *normals;
  19. polygons_struct *polygons;
  20. VIO_STR obj_filename, mnc_filename, output_filename;
  21. FILE *file;
  22. VIO_Point *points;
  24. /* get input arguments */
  25. initialize_argument_processing(argc, argv);
  26. if (!get_string_argument(NULL, &obj_filename) ||
  27. !get_string_argument(NULL, &mnc_filename) ||
  28. !get_string_argument(NULL, &output_filename)) {
  29. fprintf(stderr, "Usage: object_volume_dot_product polyhedra.obj displacement.mnc output.txt\n");
  30. return(1);
  31. }
  33. /* open the obj file */
  34. if (input_graphics_file(obj_filename,
  35. &format, &n_objects, &objects ) != VIO_OK ) {
  36. return( 1 );
  37. }
  39. /* make sure data is polygons */
  40. if( n_objects != 1 || get_object_type(objects[0]) != POLYGONS ) {
  41. fprintf(stderr, "File must contain exactly 1 polygons struct.\n" );
  42. return( 1 );
  43. }
  45. polygons = get_polygons_ptr(objects[0]);
  46. n_points = get_object_points(objects[0], &points);
  47. normals = polygons->normals;
  49. /* open the displacement volume */
  50. if (input_volume(mnc_filename, 4, NULL, MI_ORIGINAL_TYPE, FALSE, 0.0, 0.0,
  51. TRUE, &grid_volume, (minc_input_options *)NULL) != VIO_OK) {
  52. return(1);
  53. }
  54. get_volume_sizes(grid_volume, sizes);
  56. /* open the output file */
  57. if( open_file(output_filename, WRITE_FILE, ASCII_FORMAT, &file ) != VIO_OK ) {
  58. return( 1 );
  59. }
  61. for (i = 0; i < n_points; i++) {
  62. evaluate_volume_in_world(grid_volume, Point_x(points[i]),
  63. Point_y(points[i]), Point_z(points[i]),
  64. -1, TRUE, 0.0, interp_values,
  65. NULL, NULL, NULL, NULL, NULL, NULL,
  66. NULL, NULL, NULL);
  68. dot_product = Vector_x(normals[i]) * interp_values[0];
  69. dot_product += Vector_y(normals[i]) * interp_values[1];
  70. dot_product += Vector_z(normals[i]) * interp_values[2];
  73. /*
  74. printf("%f %f %f %f %f %f %f\n", Vector_x(normals[i]),
  75. Vector_y(normals[i]), Vector_z(normals[i]),
  76. interp_values[0], interp_values[1], interp_values[2],
  77. dot_product);
  78. */
  80. (void) output_real(file, dot_product);
  81. (void) output_newline(file);
  82. }
  84. (void) close_file(file);
  85. return(0);
  86. }

object_volume_dot_product.c at commit 0bfb834, under BSD-3-Clause · at the source

Overview

Authors: Nadia Blostein1,2,3, Gabriel A Devenyi1,4, Sejal Patel1,5, Raihaan Patel1,6, Stephanie Tullo1,2, Eric Plitman1,4, Manuela Costantino1,7, Ross Markello2, Olivier Parent1,2, Saashi A Bedford1,8, Chet C Sherwood9, William D Hopkins10, Alyssa Dai1,2, Jakob Seidlitz11,12, Armin Raznahan13, M Mallar Chakravarty1,2,4,6
ORCID iDs: Nadia Blostein, Gabriel A Devenyi, Manuela Costantino, Ross Markello, Olivier Parent, Chet C Sherwood, William D Hopkins, Alyssa Dai, Jakob Seidlitz, Armin Raznahan
13 affiliations
  1. Cerebral Imaging Centre, Douglas Mental Health University Institute, Verdun, QC Canada
  2. Integrated Program in Neuroscience, McGill University, Montreal, QC Canada
  3. NeuroPoly, Polytechnique Montreal, Montreal, QC Canada
  4. Department of Psychiatry, McGill University, Montreal, QC Canada
  5. Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, On Canada
  6. Department of Biological and Biomedical Engineering, McGill University, Montreal, QC Canada
  7. Undergraduate program in Neuroscience, McGill University, Montreal, QC Canada
  8. Autism Research Centre, University of Cambridge, Cambridge, UK
  9. Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
  10. Department of Comparative Medicine, University of Texas MD Anderson Cancer Center, Bastrop, TX USA
  11. Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
  12. Lifespan Brain Institute of the Children’s Hospital of Philadelphia and Penn Medicine, Philadelphia, PA USA
  13. National Institute of Mental Health, United States Department of Health and Human Services, North Bethesda, MD USA
Institutions: Douglas Mental Health University Institute (Canada); Polytechnique Montréal (Canada); McGill University (Canada); Centre for Addiction and Mental Health (Canada); University of Cambridge (United Kingdom); George Washington University (United States); The University of Texas MD Anderson Cancer Center (United States); Children's Hospital of Philadelphia (United States); University of Pennsylvania Health System (United States); University of Pennsylvania (United States); United States Department of Health and Human Services (United States); National Institute of Mental Health (United States)
Journal: Communications biology, volume 9, issue 1, article 852
Dates: received 23 June 2025; accepted 6 April 2026; published online 21 April 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s42003-026-10066-6 · PMID 42014585 · PMCID PMC13284390 · OpenAlex W7155102164
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), non-human primate (organism), cognitive (subfield)
Methods: Connectivity, Statistics, Preprocessing, Machine learning, Smoothing, state filtering, decompositions
Keywords: Computational neuroscience, Cognitive neuroscience
MeSH: Brain*, Pan troglodytes*, Thalamus*, Adult, Animals, Female, Humans, Magnetic Resonance Imaging, Male, Species Specificity (* major topic)
Topic: Functional Brain Connectivity Studies (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada; Fonds de Recherche du Québec-Société et Culture; Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre
Citations: cited by 1 paper (Europe PMC); 152 references in the paper

Abstract

There has been significant research on cortical reorganization in human evolution, but much less is known about the reorganization of subcortical circuits, key partners of the cortex. Here, using advanced image analysis and comparative neuroimaging, we systematically map organizational differences in striatal, pallidal, and thalamic anatomy between humans and chimpanzees. We relate interspecies differences—proxies for evolutionary change—to genetics and behavioral correlates in humans. We show highly heritable morphological measures are expanded across species, contrasting previous cortical findings. Multivariate techniques identified morphological-cognitive latent variables linked to striatal expansion and affective variables specifically associated with conserved thalamic and pallidal regions. Our results confirm that regions tied to higher-order cognitive functions are expanded in humans, whereas regions linked to lower-order limbic functions are conserved. These findings provide new insights into subcortical architecture. Additionally, we developed tools to map neuroimaging data across species, a prerequisite for quantitatively translating animal neuroanatomy to humans.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 5 matches between paragraphs and lines of code.

CoBrALab/MAGeTbrain

License: other
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: db4a7b1446d64d0cfd099e882d351f0d423cf4e2, 18 June 2024
Languages: Python (3), Shell (2)
Size: 23 files, 5 scripts
Software Heritage: not archived
Found in: the text, “Interspecies analysis: human average MRI templat”
Holds: README, license file, documentation
Not found: CITATION.cff, environment file, tests, continuous integration
Tools: NumPy (2 files)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
7 files
At the source: github.com/CoBrALab/MAGeTbrain

mouse-imaging-centre/minc-stuffs

License: BSD-3-Clause
State: the link answers, verified on 29 September 2026
Evidence: files inventoried
Commit: 0bfb834896e91a540774607ca7817ca8fcf41573, 22 November 2019
Languages: C (7), Python (4), Perl (2), C/C++ (2), Shell (1)
Size: 54 files, 16 scripts
Software Heritage: not archived
Found in: the text, “Interspecies analysis: vertex-wise shape differe”
Holds: README, license file, environment (setup.py)
Not found: CITATION.cff, tests, continuous integration, documentation
Tools: NumPy (3 files), SciPy (1 file)
Availability: 1 check, the latest on 29 September 2026: the link answers
  • 29 September 2026: the link answers
18 files
At the source: github.com/Mouse-Imaging-Centre/minc-stuffs/blob/master/src/object_volume_dot_product.c

rmarkello/pyls

License: GPL-2.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: d8a19d564cc5804249527b68c937df3a5fd8c7cc, 4 November 2019
Languages: Python (32)
Size: 65 files, 32 scripts
Software Heritage: archived
Found in: the text, “Intraspecies analysis: partial least squares cor”
Holds: README, license file, environment (requirements.txt, setup.cfg, setup.py, docs/requirements.txt), tests, continuous integration, documentation
Not found: CITATION.cff
Tools: NumPy (18 files), scikit-learn (4 files), h5py (2 files), pandas (2 files), SciPy (2 files), seaborn (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
34 files
At the source: github.com/rmarkello/pyls

spin-test/spin-test

License: MIT
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: d149e273f2dcfb3d1d3e86c4ec7293dd9e38e265, 25 August 2020
Languages: MATLAB (87)
Size: 120 files, 87 scripts
Software Heritage: archived
Found in: the text, “Spin-test between subcortical structure surface ”
Holds: README, license file, 1 notebook
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: FreeSurfer (3 files)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
89 files
At the source: github.com/spin-test/spin-test

Tracing map

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What the map holds:

  • 4 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 140 scripts, each with its path and the digest of its content;
  • 5 matches between paragraphs of the paper and lines of the code (method lexical-v1);
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data availability

All numerical source data underlying the figures and charts in this study have been deposited in the Zenodo repository and are publicly available at https://zenodo.org/records/19196386 under 10.5281/zenodo.19196386152. The Human Connectome Project (HCP) data used in this study are available from the Human Connectome Project repository (https://db.humanconnectome.org), subject to data use terms and registration. Chimpanzee MRI data were obtained from the National Chimpanzee Brain Resource and are accessible through the original data providers in accordance with their data-sharing policies.

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, 16 authors, 2 keywords, 10 MeSH terms, 3 funders, 140 references.

Cite

This paper

Blostein, N., Devenyi, G. A., Patel, S., Patel, R., Tullo, S., Plitman, E., Costantino, M., Markello, R., Parent, O., Bedford, S. A., Sherwood, C. C., Hopkins, W. D., Dai, A., Seidlitz, J., Raznahan, A., & Chakravarty, M. M. (2026). Morphological and anatomical variations in subcortical anatomy between humans and chimpanzees associated with heritability patterns related to human behavioral traits. Communications biology, 9(1), 852. https://doi.org/10.1038/s42003-026-10066-6

BibTeX

@article{blostein2026morphological,
author = {Blostein, Nadia and Devenyi, Gabriel A and Patel, Sejal and Patel, Raihaan and Tullo, Stephanie and Plitman, Eric and Costantino, Manuela and Markello, Ross and Parent, Olivier and Bedford, Saashi A and Sherwood, Chet C and Hopkins, William D and Dai, Alyssa and Seidlitz, Jakob and Raznahan, Armin and Chakravarty, M Mallar},
title = {{Morphological and anatomical variations in subcortical anatomy between humans and chimpanzees associated with heritability patterns related to human behavioral traits}},
journal = {Communications biology},
year = {2026},
month = apr,
volume = {9},
number = {1},
pages = {852},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/s42003-026-10066-6},
url = {https://doi.org/10.1038/s42003-026-10066-6},
pmid = {42014585},
pmcid = {PMC13284390}
}

RIS

TY - JOUR
AU - Blostein, Nadia
AU - Devenyi, Gabriel A
AU - Patel, Sejal
AU - Patel, Raihaan
AU - Tullo, Stephanie
AU - Plitman, Eric
AU - Costantino, Manuela
AU - Markello, Ross
AU - Parent, Olivier
AU - Bedford, Saashi A
AU - Sherwood, Chet C
AU - Hopkins, William D
AU - Dai, Alyssa
AU - Seidlitz, Jakob
AU - Raznahan, Armin
AU - Chakravarty, M Mallar
TI - Morphological and anatomical variations in subcortical anatomy between humans and chimpanzees associated with heritability patterns related to human behavioral traits
T2 - Communications biology
J2 - Commun Biol
PY - 2026
DA - 2026/04/21
VL - 9
IS - 1
SP - 852
SN - 2399-3642
PB - Nature Publishing Group
DO - 10.1038/s42003-026-10066-6
UR - https://doi.org/10.1038/s42003-026-10066-6
LA - en
ER -

CSL-JSON

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"container-title": "Communications biology",
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{
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{
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