Baby Open Brains: An Open-Source Repository of Infant Brain Segmentations

Feczko, E. J.; Stoyell, S. M.; Moore, L. A.; Alexopoulos, D.; Bagonis, M.; Barrett, K.; Bower, B.; Cavender, A.; Chamberlain, T. A.; Conan, G.; Day, T. K.; Goradia, D.; Graham, A.; Heisler-Roman, L.; Hendrickson, T. J.; Houghton, A.; Kardan, O.; Kiffmeyer, E. A.; Lee, E. G.; Lundquist, J. T.; Lucena, C.; Martin, T.; Mummaneni, A.; Myricks, M.; Narnur, P.; Perrone, A. J.; Reiners, P.; Rueter, A. R.; Saw, H.; Styner, M.; Sung, S.; Tiklasky, B.; Wisnowski, J. L.; Yacoub, E.; Zimmermann, B.; Smyser, C. D.; Rosenberg, M. D.; Fair, D. A.; Elison, J. T.

doi:10.1101/2024.10.02.616147

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bioRxiv · 10.1101/2024.10.02.616147

Baby Open Brains: An Open-Source Repository of Infant Brain Segmentations

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Abstract

Reproducibility of neuroimaging research on infant brain development remains limited due to highly variable protocols and processing approaches. Progress towards reproducible pipelines is limited by a lack of benchmarks such as gold standard brain segmentations. Addressing this core limitation, we constructed the Baby Open Brains (BOBs) Repository, an open source resource comprising manually curated and expert-reviewed infant brain segmentations. Markers and expert reviewers manually segmented anatomical MRI data from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Anatomical images showed dramatic differences in myelination and intensities across the 1 to 9 month age range, emphasizing the need for densely sampled gold standard manual segmentations in these ages. The BOBs repository is publicly available through the Masonic Institute for the Developing Brain (MIDB) Open Data Initiative, which links S3 storage, Datalad for version control, and BrainBox for visualization. This repository represents an open-source paradigm, where new additions and changes can be added, enabling a community-driven resource that will improve over time and extend into new ages and protocols. These manual segmentations and the ongoing repository provide a benchmark for evaluating and improving pipelines dependent upon segmentations in the youngest populations. As such, this repository provides a vitally needed foundation for early-life large-scale studies such as HBCD.

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Feczko, E. J., Stoyell, S. M., Moore, L. A., Alexopoulos, D., Bagonis, M., Barrett, K., Bower, B., Cavender, A., Chamberlain, T. A., Conan, G., Day, T. K., Goradia, D., Graham, A., Heisler-Roman, L., Hendrickson, T. J., Houghton, A., Kardan, O., Kiffmeyer, E. A., Lee, E. G., Lundquist, J. T., Lucena, C., Martin, T., Mummaneni, A., Myricks, M., Narnur, P., Perrone, A. J., Reiners, P., Rueter, A. R., Saw, H., Styner, M., Sung, S., Tiklasky, B., Wisnowski, J. L., Yacoub, E., Zimmermann, B., Smyser, C. D., Rosenberg, M. D., Fair, D. A., Elison, J. T.. 2024-10-03. Baby Open Brains: An Open-Source Repository of Infant Brain Segmentations. https://doi.org/10.1101/2024.10.02.616147

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