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Peer-reviewedCC BY 4.0Developmental Cognitive Neuroscience

Diffusion MRI processing in the HEALthy Brain and Child Development study: Innovations and applications

  • Matthew Cieslak1,2,3
  • M. Okan Irfanoglu4,5
  • Steven L. Meisler1,2,3
  • Taylor Salo1,2,3
  • Adam C. Raikes6
  • Philip A. Cook7
  • Ai Wern Chung8,9,10
  • Erik G. Lee11,12,13
  • Ruolin Li14,15
  • Xu Li16,17
  • Diliana Pecheva18
  • Damien A. Fair11,19,20
7 more authors
  • Christopher D. Smyser21,22,23,24,25
  • Michael P. Harms24
  • Bennett A. Landman26
  • Jessica L. Wisnowski27,28
  • Hao Huang14,29
  • Andrew L. Alexander30
  • Theodore D. Satterthwaite1,2,3
30 affiliations
  1. 1Penn Lifespan Informatics and Neuroimaging Center (PennLINC), Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
  2. 2Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
  3. 3Lifespan Brain Institute (LiBI), The Children’s Hospital of Philadelphia and Perelman School of Medicine, Philadelphia, PA, United States
  4. 4National Institute of Biomedical Imaging and Bioengineering, Bethesda, MD, United States
  5. 5National Institutes of Health, Bethesda, MD, United States
  6. 6Center for Innovation in Brain Science, University of Arizona, Tucson, AZ, United States
  7. 7PICSL Lab, Department of Radiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, United States
  8. 8Fetal-Neonatal Neuroimaging and Developmental Science Center, Boston Children's Hospital, Boston, MA, United States
  9. 9Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
  10. 10Department of Pediatrics, Harvard Medical School, Boston, MA, United States
  11. 11Masonic Institute for the Developing Brain, University of Minnesota, Minneapolis, MN, United States
  12. 12Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, United States
  13. 13Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, United States
  14. 14Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, PA, United States
  15. 15Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
  16. 16F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, United States
  17. 17Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
  18. 18Center for Multimodal Imaging and Genetics, J. Craig Venter Institute, La Jolla, CA, United States
  19. 19Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, United States
  20. 20Institute of Child Development, College of Education and Human Development, University of Minnesota, Minneapolis, MN, United States
  21. 21Department of Neurology, Washington University in St. Louis, St. Louis, MO, United States
  22. 22Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, United States
  23. 23Department of Radiology, Washington University in St. Louis, St. Louis, MO, United States
  24. 24Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, United States
  25. 25Department of Neurosurgery, Washington University in St. Louis, St. Louis, MO, United States
  26. 26Vanderbilt University, Nashville, TN, United States
  27. 27The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, United States
  28. 28Department of Pediatrics, University of Southern California, Los Angeles, CA, United States
  29. 29Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
  30. 30University of Wisconsin – Madison, Madison, WI, United States
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Abstract

The landmark ongoing HEALthy Brain and Child Development (HBCD) study will longitudinally chart brain development in a large sample (projected n = 7200) of infants through age 10 years with multimodal neuroimaging that includes an advanced diffusion MRI (dMRI) acquisition. Here, we detail advances in dMRI image processing developed for HBCD, incorporated into the widely used QSIPrep pipeline. Major changes to preprocessing include improvements in infant brain extraction, distortion correction, and normalization to infant-specific templates. Additionally, we describe a new software package – QSIRecon – that yields rich derived data including diverse maps of tissue microstructure as well as person-specific white matter bundles. Using dMRI data from a subset of the HBCD 1.0 release where age information was available (n = 529 sessions across two time points), we observe critical improvements in data quality with preprocessing and see expected developmental patterns. Moving forward, the publicly-available data from HBCD will rapidly grow to become the largest study of brain development in infancy and early childhood using dMRI. QSIPrep and QSIRecon are openly available and can be applied to other infant and pediatric dMRI datasets.

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Cite

BibTeXRIS
BibTeX
@article{cieslak2026diffusion,
  title = {{Diffusion MRI processing in the HEALthy Brain and Child Development study: Innovations and applications}},
  author = {Matthew Cieslak and M. Okan Irfanoglu and Steven L. Meisler and Taylor Salo and Adam C. Raikes and Philip A. Cook and Ai Wern Chung and Erik G. Lee and Ruolin Li and Xu Li and Diliana Pecheva and Damien A. Fair and Christopher D. Smyser and Michael P. Harms and Bennett A. Landman and Jessica L. Wisnowski and Hao Huang and Andrew L. Alexander and Theodore D. Satterthwaite},
  journal = {Developmental Cognitive Neuroscience},
  year = {2026},
  month = oct,
  doi = {10.1016/j.dcn.2026.101838},
  url = {https://doi.org/10.1016/j.dcn.2026.101838},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Diffusion MRI processing in the HEALthy Brain and Child Development study: Innovations and applications
AU  - Matthew Cieslak
AU  - M. Okan Irfanoglu
AU  - Steven L. Meisler
AU  - Taylor Salo
AU  - Adam C. Raikes
AU  - Philip A. Cook
AU  - Ai Wern Chung
AU  - Erik G. Lee
AU  - Ruolin Li
AU  - Xu Li
AU  - Diliana Pecheva
AU  - Damien A. Fair
AU  - Christopher D. Smyser
AU  - Michael P. Harms
AU  - Bennett A. Landman
AU  - Jessica L. Wisnowski
AU  - Hao Huang
AU  - Andrew L. Alexander
AU  - Theodore D. Satterthwaite
PY  - 2026
DA  - 2026/10/15
JO  - Developmental Cognitive Neuroscience
DO  - 10.1016/j.dcn.2026.101838
UR  - https://doi.org/10.1016/j.dcn.2026.101838
AB  - The landmark ongoing HEALthy Brain and Child Development (HBCD) study will longitudinally chart brain development in a large sample (projected n = 7200) of infants through age 10 years with multimodal neuroimaging that includes an advanced diffusion MRI (dMRI) acquisition. Here, we detail advances in dMRI image processing developed for HBCD, incorporated into the widely used QSIPrep pipeline. Major changes to preprocessing include improvements in infant brain extraction, distortion correction, and normalization to infant-specific templates. Additionally, we describe a new software package – QSIRecon – that yields rich derived data including diverse maps of tissue microstructure as well as person-specific white matter bundles. Using dMRI data from a subset of the HBCD 1.0 release where age information was available (n = 529 sessions across two time points), we observe critical improvements in data quality with preprocessing and see expected developmental patterns. Moving forward, the publicly-available data from HBCD will rapidly grow to become the largest study of brain development in infancy and early childhood using dMRI. QSIPrep and QSIRecon are openly available and can be applied to other infant and pediatric dMRI datasets.
SN  - 1878-9293
SN  - 1878-9307
ER  -