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Brain volumes in fetuses with congenital heart disease and placental vascular abnormalities.

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  1. [1] § Methods › MRI acquisition and processing ↔ config.sh, the whole file · a weak match · score 0.68 · intermediate zone, cortical plate, subplate

Paper

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

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The authors' code

Shell · 26 lines · 860 B · no license · 1 match

  1. #!/bin/bash
  3. # Atlas location
  4. export CRLMASREF=/path/to/your/CRL2025Atlas
  6. # CRKIT location
  7. CRKIT=/path/to/your/crkit-main
  8. source ${CRKIT}/bin/crkit-env.sh
  10. # Default template image list
  11. # You can add additional atlas/reference images to the list
  12. tlist="${REPO}/tlist.txt"
  14. # # # SUFFIXES OF DEFAULT ATLAS LABELS # #
  15. # Tissue = standard tissue seg
  16. # tissueWMZ = with subplate and intermediate zone, normally only used for GA < 32 weeks
  17. # region = regional segmentation (cortical parcellation)
  18. AllLabs="tissue tissueWMZ regional"
  19. # # # # # # # # # # # # # # # # # # # # # #
  21. # # # Set segmentation to ON or OFF # # #
  22. # You can disable this setting if you only want the registrations to happen
  23. segmentation="ON"
  24. # # # # # # # # # # # # # # # # # # # # #
  25. LCP="112" # Cortical plate label used to test PVC output behavior
  26. # # # # # # # # # # # # # # # # # # # # #

config.sh at commit e899640, no license · at the source

Overview

Authors: Erin A O’Brien1, David Wypij2,3,4, Valerie Rofeberg2, Reem Chamseddine5,6, Clemente Velasco-Annis7, Kaylin Taylor8, Kaysi Herrera Pujols5, Nicholas J Hart5, Sarah U Morton2,9, Joshua Litwin5, Nankee Kumar10, Karem Kennedy10, Louise Wilkins-Haug11, Jane W Newburger2,3, Anthony O Odibo12, Ali Gholipour7,13,14, Joshua S Shimony15, Caitlin K Rollins5,16, Cynthia M Ortinau17
ORCID iDs: Erin A O’Brien, David Wypij, Sarah U Morton, Nankee Kumar, Caitlin K Rollins, Cynthia M Ortinau
17 affiliations
  1. Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN USA
  2. Department of Cardiology, Boston Children’s Hospital, Boston, MA USA
  3. Department of Pediatrics, Harvard Medical School, Boston, MA USA
  4. Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA
  5. Department of Neurology, Boston Children’s Hospital, Boston, MA USA
  6. Department of Obstetrics and Gynecology, The Brooklyn Hospital Center, Brooklyn, NY USA
  7. Department of Radiology, Boston Children’s Hospital, Boston, MA USA
  8. Department of Neurology, Washington University in St. Louis School of Medicine, St. Louis, MO USA
  9. Division of Newborn Medicine, Department of Pediatrics, Boston Children’s Hospital, Boston, MA USA
  10. St. Louis Children’s Hospital, St. Louis, MO USA
  11. Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Harvard Medical School, Brigham and Women’s Hospital in Boston, Boston, MA USA
  12. Department of Obstetrics and Gynecology, University Health Truman Medical Center, Kansas City, MO USA
  13. Department of Radiological Sciences, University of California Irvine, Irvine, CA USA
  14. Department of Electrical Engineering and Computer Science, University of California Irvine, Irvine, CA USA
  15. Mallinkrodt Institute of Radiology, Washington University in St. Louis School of Medicine, St. Louis, MO USA
  16. Department of Neurology, Harvard Medical School, Boston, MA USA
  17. Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO USA
Institutions: Vanderbilt University Medical Center (United States); Boston Children's Hospital (United States); Harvard University (United States); Brooklyn Hospital Center (United States); Washington University in St. Louis (United States); St. Louis Children's Hospital (United States); Brigham and Women's Hospital (United States); Truman Medical Center (United States); University of California, Irvine (United States)
Journal: Journal of perinatology : official journal of the California Perinatal Association, volume 46, issue 7, pages 1155-1163
Dates: received 2 December 2024; accepted 25 February 2026; published online 13 March 2026; in print 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41372-026-02601-4 · PMID 41826659 · PMCID PMC13267945 · OpenAlex W7135226829
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), structural MRI / diffusion (modality), human (organism)
Methods: Statistics, Preprocessing
Keywords: Developmental neurogenesis, Genetic testing, Congenital heart defects
MeSH: Brain*, Heart Defects, Congenital*, Placenta*, Placenta Diseases*, Adult, Female, Fetus, Humans, Magnetic Resonance Imaging, Organ Size, Pregnancy, Prospective Studies (* major topic)
Topic: Congenital Heart Disease Studies (Epidemiology, Medicine), according to OpenAlex
Funding: NHLBI NIH HHS (K23 HL141602, T32 HL125241, K08 HL157653); NIBIB NIH HHS (R01 EB031849, R01 EB032366); U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) (U54HD087011); U.S. Department of Health & Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB) (R01EB031849, R01EB032366); NINDS NIH HHS (K23 NS101120); U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI) (K08HL157653, K23HL141602); U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS) (K23NS101120); NICHD NIH HHS (U54 HD087011)
Citations: cited by 3 papers (Europe PMC); 51 references in the paper

Abstract

Objective: Investigate the association between placental vascular abnormalities and regional brain volumes in congenital heart disease (CHD) fetuses with and without genetic abnormalities.

Study design: Secondary analysis of brain magnetic resonance imaging (MRI) and placental pathology data from 121 CHD fetuses enrolled in prospective neuroimaging studies at two centers.

Results: Placental vascular abnormality was present in 46% of fetuses, and genetic abnormality was present in 19%, including 12% with both abnormalities. Fetuses with the combination of placental and genetic abnormalities had smaller brain volumes compared to fetuses without either abnormality for total brain, subcortical gray matter, brainstem, and cerebellum, with a significant interaction (P < 0.05) between placental and genetic abnormalities for intracranial and subcortical gray matter volumes.

Conclusion: Smaller brain volumes for CHD fetuses with placental and genetic abnormalities may suggest common genetic pathways affect placental, heart, and brain development, or that genetic abnormalities heighten vulnerability when placental changes occur.

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 1 match between paragraphs and lines of code.

IntelligentImaging/CRL-2025-MAS

License: none: the authors keep all their rights
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: e89964027bc381e28ce0f41f52ec7c74775ea0c6, 7 May 2026
Languages: Shell (9)
Size: 17 files, 9 scripts
Software Heritage: not archived
Found in: the text, “MRI acquisition and processing”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: MRtrix3 (2 files), ANTs (1 file), FSL (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
10 files
At the source: github.com/IntelligentImaging/CRL-2025-MAS

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;
  • 9 scripts, each with its path and the digest of its content;
  • 1 match 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

Datasets cited

Data availability

The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

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, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 19 authors, 3 keywords, 12 MeSH terms, 8 funders, 51 references.

Cite

This paper

O’Brien, E. A., Wypij, D., Rofeberg, V., Chamseddine, R., Velasco-Annis, C., Taylor, K., Herrera Pujols, K., Hart, N. J., Morton, S. U., Litwin, J., Kumar, N., Kennedy, K., Wilkins-Haug, L., Newburger, J. W., Odibo, A. O., Gholipour, A., Shimony, J. S., Rollins, C. K., & Ortinau, C. M. (2026). Brain volumes in fetuses with congenital heart disease and placental vascular abnormalities. Journal of perinatology : official journal of the California Perinatal Association, 46(7), 1155-1163. https://doi.org/10.1038/s41372-026-02601-4

BibTeX

@article{obrien2026brain,
author = {O’Brien, Erin A and Wypij, David and Rofeberg, Valerie and Chamseddine, Reem and Velasco-Annis, Clemente and Taylor, Kaylin and Herrera Pujols, Kaysi and Hart, Nicholas J and Morton, Sarah U and Litwin, Joshua and Kumar, Nankee and Kennedy, Karem and Wilkins-Haug, Louise and Newburger, Jane W and Odibo, Anthony O and Gholipour, Ali and Shimony, Joshua S and Rollins, Caitlin K and Ortinau, Cynthia M},
title = {{Brain volumes in fetuses with congenital heart disease and placental vascular abnormalities}},
journal = {Journal of perinatology : official journal of the California Perinatal Association},
year = {2026},
month = mar,
volume = {46},
number = {7},
pages = {1155--1163},
publisher = {Springer Nature},
issn = {0743-8346},
doi = {10.1038/s41372-026-02601-4},
url = {https://doi.org/10.1038/s41372-026-02601-4},
pmid = {41826659},
pmcid = {PMC13267945}
}

RIS

TY - JOUR
AU - O’Brien, Erin A
AU - Wypij, David
AU - Rofeberg, Valerie
AU - Chamseddine, Reem
AU - Velasco-Annis, Clemente
AU - Taylor, Kaylin
AU - Herrera Pujols, Kaysi
AU - Hart, Nicholas J
AU - Morton, Sarah U
AU - Litwin, Joshua
AU - Kumar, Nankee
AU - Kennedy, Karem
AU - Wilkins-Haug, Louise
AU - Newburger, Jane W
AU - Odibo, Anthony O
AU - Gholipour, Ali
AU - Shimony, Joshua S
AU - Rollins, Caitlin K
AU - Ortinau, Cynthia M
TI - Brain volumes in fetuses with congenital heart disease and placental vascular abnormalities
T2 - Journal of perinatology : official journal of the California Perinatal Association
J2 - J Perinatol
PY - 2026
DA - 2026/03/13
VL - 46
IS - 7
SP - 1155
EP - 1163
SN - 0743-8346
PB - Springer Nature
DO - 10.1038/s41372-026-02601-4
UR - https://doi.org/10.1038/s41372-026-02601-4
LA - en
ER -

CSL-JSON

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