Funding Sources🔗
This work was supported by the National Institutes of Health (NIH) through awards administered by the National Institute on Drug Abuse (NIDA) (1U01DA055371 The Healthy Brain and Child Development National Consortium; U24 DA055330 Healthy brain and child development national consortium data coordinating center; U01DA041148 Consortium Research Project Site at OHSU), Office of the Director (OD) (UG3 OD023349 Pre- and Postnatal Exposure Periods for Child Health: Common Risks and Shared Mechanisms), and National Institute of Mental Health (NIMH) (1R37MH125829-01 Precision mapping of individualized executive networks in youth; 2R01MH096773-08A1 Identification of outcome-based sub-populations using deep phenotyping and precision functional mapping across ADHD and ASD).
Software🔗
- nvidia/pytorch:21.11-py3
- nnU-Net
- SynthSeg
- FSL v6.0.5.1
- ANTS v2.3.3
- BIBSnet v1.0.0
- SynthStrip v1.5
References🔗
Avants, Tustison, and Song. n.d. "Advanced Normalization Tools (ANTS)." The Insight Journal. https://scicomp.ethz.ch/public/manual/ants/2.x/ants2.pdf.
Billot, Benjamin, Douglas N. Greve, Oula Puonti, Axel Thielscher, Koen Van Leemput, Bruce Fischl, Adrian V. Dalca, and Juan Eugenio Iglesias. 2021. "SynthSeg: Domain Randomisation for Segmentation of Brain Scans of Any Contrast and Resolution." arXiv [eess.IV]. arXiv. http://arxiv.org/abs/2107.09559.
Hoopes, Andrew, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl, Malte Hoffmann (*equal contribution). 2022. "SynthStrip: Skull-Stripping for Any Brain Image." NeuroImage 260. https://doi.org/10.1016/j.neuroimage.2022.119474.
Howell, Brittany R., Martin A. Styner, Wei Gao, Pew-Thian Yap, Li Wang, Kristine Baluyot, Essa Yacoub, et al. 2019. "The UNC/UMN Baby Connectome Project (BCP): An Overview of the Study Design and Protocol Development." NeuroImage 185 (January): 891–905.
Isensee, Fabian, Paul F. Jaeger, Simon A. A. Kohl, Jens Petersen, and Klaus H. Maier-Hein. 2021. "nnU-Net: A Self-Configuring Method for Deep Learning-Based Biomedical Image Segmentation." Nature Methods 18 (2): 203–11.
Jenkinson, Mark, Christian F. Beckmann, Timothy E. J. Behrens, Mark W. Woolrich, and Stephen M. Smith. 2012. "FSL." NeuroImage 62 (2): 782–90.
Kelley, William, Nathan Ngo, Adrian V. Dalca, Bruce Fischl, Lilla Zöllei, Malte Hoffmann (*equal contribution). 2024. "IEEE International Symposium on Biomedical Imaging (ISBI)". https://arxiv.org/abs/2402.16634.
Paszke, Adam, Sam Gross, Soumith Chintala, Gregory Chanan, Edward Yang, Zachary DeVito, Zeming Lin, Alban Desmaison, Luca Antiga, and Adam Lerer. 2017. "Automatic Differentiation in PyTorch." https://openreview.net/pdf?id=BJJsrmfCZ.