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Spatiotemporal white-matter development across early childhood.

Code ↔ Paper

6 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 6 matches · 5 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Materials and methods › Diffusion MRI processing › Single-shell 3-tissue CSD & fixel-based analysis ↔ A_FBA-pipeline/1_SS3TCSD_PopTemplate/1_SS3T-CSD_merv_grp_avg_rf.sh, the whole file · a weak match · score 0.95 · SS3T CSD, tissue Constrained Spherical, Single shell, intensity normalized, Deconvolution, FODs
  2. [2] § Materials and methods › Diffusion MRI processing › Bundle-specific tractography ↔ A_FBA-pipeline/2_Tractography/TractSeg_script_template_grp_avg_rf.sh, the whole file · a weak match · score 0.77 · TractSeg, template space, tractography, TOMs, tracking, peak
  3. [3] § Materials and methods › Diffusion MRI processing › Bundle-specific tractography ↔ A_FBA-pipeline/4_WarpSubj2Templat_WB_fixel_metrics/Create_wb_fixels_maps_grp_avg_rf.sh, the whole file · a weak match · score 0.62 · voxel masks, template space, peak, FOD, maps, tracts
  4. [4] § Materials and methods › Diffusion MRI processing › Single-shell 3-tissue CSD & fixel-based analysis ↔ A_FBA-pipeline/4_WarpSubj2Templat_WB_fixel_metrics/Create_wb_fixels_maps_grp_avg_rf.sh, the whole file · a weak match · score 0.60 · template space, warped, density, FOD, cross, metric
  5. [5] § Materials and methods › Diffusion MRI processing › Preprocessing ↔ A_FBA-pipeline/1_SS3TCSD_PopTemplate/1_SS3T-CSD_merv_grp_avg_rf.sh, the whole file · a weak match · score 0.58 · MRtrix3Tissue, bias field, Diffusion
  6. [6] § Materials and methods › Diffusion MRI processing › Quality assessment ↔ A_FBA-pipeline/6_FixelThresholding/1_FD/3_Threshold_FD_maps_grp_avg_rf.sh, lines 1–42 · score 0.51 · thresholded FD maps, fixel, log, masks, Segment, tract

Paper

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

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The authors' code

Shell · 36 lines · 1.8 KB · no license · 2 matches

  1. #!/bin/sh
  3. #########################################################################################################################
  5. # SINGLE SHELL 3-TISSUE CONSTRAINED SPHERICAL DECONVOLUTION # - Using group averaged response functions
  7. #########################################################################################################################
  9. # This script utilizes MRtrix3Tissue
  11. cd /PATH/TO/DIRECTORY
  13. # Set the base directory path
  14. sub_dir='/PATH/TO/DIRECTORY/subjects'
  16. # Iterate over each subject directory
  17. for subj in "$sub_dir"/*;
  18. do
  19. # Print a message indicating the current subject being processed
  20. echo "Processing $subj"
  22. # Perform DWI (Diffusion-Weighted Imaging) SS3TCSD steps
  24. # Estimate response functions using the Dhollander algorithm
  25. #dwi2response dhollander $subj/dwi.bias.1.25mm.mif $subj/response_wm.txt $subj/response_gm.txt $subj/response_csf.txt -force
  27. # Perform single-shell 3-tissue CSD (Constrained Spherical Deconvolution) - Using group averaged response functions
  28. ss3t_csd_beta1 $subj/dwi.bias.1.25mm.mif ../group_average_response_wm.txt $subj/wmfod_grpavg.mif ../group_average_response_gm.txt $subj/gm_grpavg.mif ../group_average_response_csf.txt $subj/csf_grpavg.mif -mask $subj/dwi.bias.1.25mm.mask.mif -force
  30. # Perform joint bias field and intensity normalization - Using group averaged response functions
  31. mtnormalise $subj/wmfod_grpavg.mif $subj/wmfod_grpavg_norm.mif $subj/gm_grpavg.mif $subj/gm_grpavg_norm.mif $subj/csf_grpavg.mif $subj/csf_grpavg_norm.mif -mask $subj/dwi.bias.1.25mm.mask.mif -force
  33. # Generate FOD-based directionally-encoded colour (DEC) map - Using group averaged response functions
  34. fod2dec $subj/wmfod_grpavg_norm.mif $subj/wmdec_grpavg_norm.mif -mask $subj/dwi.bias.1.25mm.mask.mif -force
  36. done

1_SS3T-CSD_merv_grp_avg_rf.sh at commit 5bb06e8, no license · at the source

Overview

Authors: Mervyn Singh1,2,3, Dennis Dimond4, Deborah Dewey1,2,5,6, Catherine Lebel1,2,3,5, Signe Bray1,2,3
ORCID iDs: Mervyn Singh, Deborah Dewey, Signe Bray
  1. Child and Adolescent Imaging Research (CAIR) Program, Alberta Children’s Research Institute, University of Calgary, 28 Oki Dr, Calgary, Alberta, T3B 6A8, Canada
  2. Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr NW, Calgary, Alberta, T2N 4N1, Canada
  3. Department of Radiology, Cumming School of Medicine, 3330 Hospital Dr NW, Calgary, Alberta, T2N 4N1, Canada
  4. Department of Radiology, University of British Columbia, 2775 Laurel Street, Vancouver, British Columbia, V5Z 1M9, Canada
  5. Department of Paediatrics, Cumming School of Medicine, University of Calgary, 28 Oki Dr, Calgary, Alberta, T3B 6A8, Canada
  6. Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW Calgary, Alberta, T2N 4Z6, Canada
Institutions: University of Calgary (Canada); Hotchkiss Brain Institute (Canada); University of British Columbia (Canada)
Journal: Cerebral cortex (New York, N.Y. : 1991), volume 36, issue 9, article bhag132
Dates: received 13 March 2026; accepted 28 July 2026; published online 3 September 2026; in print September 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1093/cercor/bhag132 · PMID 42691503 · PMCID PMC13541283 · OpenAlex W7207614293
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: structural MRI / diffusion (modality), human (organism), developmental (subfield)
Methods: Connectivity, Statistics, Preprocessing, fMRI & imaging
Keywords: Along-tract, Diffusion MRI, Early childhood, Fixel-based analysis, Neurodevelopment
MeSH: Brain*, Child Development*, White Matter*, Child, Child, Preschool, Diffusion Magnetic Resonance Imaging, Diffusion Tensor Imaging, Female, Humans, Longitudinal Studies, Male, Neural Pathways, Neurodevelopment (* major topic)
Topic: Advanced Neuroimaging Techniques and Applications (Radiology, Nuclear Medicine and Imaging, Medicine), according to OpenAlex
Funding: Canadian Institutes of Health Research; Natural Sciences and Engineering Research Council of Canada; Canada Research Chair Program; Harley Hotchkiss - Samuel Weiss Postdoctoral Fellowship
Citations: not cited yet (Europe PMC); 82 references in the paper

Abstract

Early childhood development is scaffolded by rapid maturation of brain white matter structure, believed to support the emergence of cognitive and socioemotional functions. Previous whole-tract studies have suggested patterns of white matter development occurring along posterior–anterior, deep–superficial, and inferior–superior axes. However, these have largely been cross-sectional and employed nonspecific metrics of white matter organization. Using longitudinal diffusion imaging data from 133 children (4 to 8 years; 76 females), the present work characterizes along-tract patterns of white matter development across association, commissural, and projection bundles using fixel-based analysis. Within long range association bundles, faster age-related changes were observed for segments adjacent to the visual cortices relative to segments located near association regions, supporting a sensorimotor-association axis of brain development. An inferior–superior pattern was found for projection tracts, with faster age-effects observed for segments near the brainstem. Lastly, while several association and commissural bundles exhibited faster maturation within central segments; indicative of a deep-superficial axis, effects were mixed between micro- and macrostructure, underscoring the unique developmental timing of these different fiber properties. Our findings provide evidence that within-tract white matter maturation unfolds along key spatiotemporal axes, and suggests that increased spatial precision can advance our understanding of early childhood brain development.

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

Repository

Its files are read in the Code ↔ Paper reader above, with 6 matches between paragraphs and lines of code.

MervSingh/alongtract_fba_wm_dev

License: none: the authors keep all their rights
State: the link answers, verified on 26 September 2026
Evidence: files inventoried
Commit: 5bb06e833695564328ade89fbda01abe9fc1c939, 21 July 2026
Languages: Python (25), R (24), Shell (16), MATLAB (1)
Size: 86 files, 66 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: tidyverse (24 files), Matplotlib (23 files), pandas (20 files), NumPy (19 files), MRtrix3 (15 files), patchwork (14 files), broom (13 files), NiBabel (9 files), ggplot2 (8 files), scikit-image (8 files), lme4 (4 files), lmerTest (4 files), seaborn (2 files), ANTs (1 file), DIPY (1 file), FSL (1 file)
Availability: 1 check, the latest on 26 September 2026: the link answers
  • 26 September 2026: the link answers
67 files
At the source: github.com/MervSingh/alongtract_fba_wm_dev.git

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;
  • 66 scripts, each with its path and the digest of its content;
  • 6 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

Due to ethical considerations, public sharing of the raw data is not permitted but may be provided upon reasonable request by contacting the senior corresponding author (S. Bray). This policy is in accordance with the funding bodies that supported this research and the Conjoint Health and Research Ethics Board at the University of Calgary. Scripts for all steps in the analysis pipeline are publicly available on GitHub: https://github.com/MervSingh/alongtract_fba_wm_dev.git

Reproduced under the paper's license (CC BY-NC), 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, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 5 keywords, 13 MeSH terms, 4 funders, 78 references.

Cite

This paper

Singh, M., Dimond, D., Dewey, D., Lebel, C., & Bray, S. (2026). Spatiotemporal white-matter development across early childhood. Cerebral cortex (New York, N.Y. : 1991), 36(9), bhag132. https://doi.org/10.1093/cercor/bhag132

BibTeX

@article{singh2026spatiotemporal,
author = {Singh, Mervyn and Dimond, Dennis and Dewey, Deborah and Lebel, Catherine and Bray, Signe},
title = {{Spatiotemporal white-matter development across early childhood}},
journal = {Cerebral cortex (New York, N.Y. : 1991)},
year = {2026},
month = sep,
volume = {36},
number = {9},
pages = {bhag132},
publisher = {Oxford University Press},
issn = {1047-3211},
doi = {10.1093/cercor/bhag132},
url = {https://doi.org/10.1093/cercor/bhag132},
pmid = {42691503},
pmcid = {PMC13541283}
}

RIS

TY - JOUR
AU - Singh, Mervyn
AU - Dimond, Dennis
AU - Dewey, Deborah
AU - Lebel, Catherine
AU - Bray, Signe
TI - Spatiotemporal white-matter development across early childhood
T2 - Cerebral cortex (New York, N.Y. : 1991)
J2 - Cereb Cortex
PY - 2026
DA - 2026/09/01
VL - 36
IS - 9
SP - bhag132
SN - 1047-3211
PB - Oxford University Press
DO - 10.1093/cercor/bhag132
UR - https://doi.org/10.1093/cercor/bhag132
LA - en
ER -

CSL-JSON

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

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