Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications

Cieslak, M.; Irfanoglu, M. O.; Meisler, S. L.; Salo, T.; Raikes, A. C.; Cook, P. A.; Chung, A. W.; Lee, E. G.; Li, R.; Li, X.; Pecheva, D.; Fair, D. A.; Smyser, C. D.; Harms, M. P.; Landman, B. A.; Wisnowski, J. L.; Huang, H.; Alexander, A. L.; Satterthwaite, T. D.

doi:10.1101/2025.11.10.687672

bioRxiv · 10.1101/2025.11.10.687672

Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications

Cieslak, M.·Irfanoglu, M. O.·Meisler, S. L.·Salo, T.·Raikes, A. C.·Cook, P. A.·Chung, A. W.·Lee, E. G.·Li, R.·Li, X.·Pecheva, D.·Fair, D. A.·Smyser, C. D.·Harms, M. P.·Landman, B. A.·Wisnowski, J. L.·Huang, H.·Alexander, A. L.·Satterthwaite, T. D.

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Abstract

The landmark ongoing HEALthy Brain and Cognitive Development (HBCD) study will longitudinally chart brain development in a large sample (projected n=7,200) 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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Cieslak, M., Irfanoglu, M. O., Meisler, S. L., Salo, T., Raikes, A. C., Cook, P. A., Chung, A. W., Lee, E. G., Li, R., Li, X., Pecheva, D., Fair, D. A., Smyser, C. D., Harms, M. P., Landman, B. A., Wisnowski, J. L., Huang, H., Alexander, A. L., Satterthwaite, T. D.. 2025-11-11. Diffusion MRI Processing in the HEALthy Brain and Child Development Study: Innovations and Applications. https://doi.org/10.1101/2025.11.10.687672

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