Author
Convolutional-recurrent neural networks approximate diffusion tractography from T1-weighted MRI and associated anatomical context
May. 29, 2023—Leon Y. Cai, Ho Hin Lee, Nancy R. Newlin, Cailey I. Kerley, Praitayini Kanakaraj, Qi Yang, Graham W. Johnson, Daniel Moyer, Kurt G. Schilling, François Rheault, and Bennett A. Landman Paper: https://www.biorxiv.org/content/10.1101/2023.02.25.530046v2 Code: https://github.com/MASILab/cornn_tractography Abstract Diffusion MRI (dMRI) streamline tractography is the gold-standard for in vivo estimation of white matter (WM) pathways in the brain. However, the...
Implementation considerations for deep learning with diffusion MRI streamline tractography
May. 29, 2023—Leon Y. Cai, Ho Hin Lee, Nancy R. Newlin, Michael E. Kim, Daniel Moyer, Francois Rheault, Kurt G. Schilling, and Bennett A. Landman Paper: https://www.biorxiv.org/content/10.1101/2023.04.03.535465v1 Code: https://github.com/MASILab/STrUDeL Abstract One area of medical imaging that has recently experienced innovative deep learning advances is diffusion MRI (dMRI) streamline tractography with recurrent neural networks (RNNs). Unlike traditional imaging studies which...
SynBOLD-DisCo: Synthetic BOLD images for distortion correction of fMRI without additional calibration scans
Nov. 13, 2022—Tian Yu*, Leon Y. Cai*, Victoria L. Morgan, Sarah E. Goodale, Dario J. Englot, Catherine E. Chang, Bennett A. Landman, and Kurt G. Schilling * Equal first authorship https://github.com/MASILab/SynBOLD-DisCo Abstract The blood oxygen level dependent (BOLD) signal from functional magnetic resonance imaging (fMRI) is a noninvasive technique that has been widely used in research to...
Batch size: go big or go home? Counterintuitive improvement in medical autoencoders with smaller batch size
Nov. 13, 2022—Cailey I. Kerley*, Leon Y. Cai*, Yucheng Tang, Lori L. Beason-Held, Susan M. Resnick, Laurie E. Cutting, and Bennett A. Landman. *Equal first authorship Abstract Batch size is a key hyperparameter in training deep learning models. Conventional wisdom suggests larger batches produce improved model performance. Here we present evidence to the contrary, particularly when using autoencoders...
Joint independent component analysis for hypothesizing spatiotemporal relationships between longitudinal gray and white matter changes in preclinical Alzheimer’s disease
Dec. 10, 2021—Leon Y. Cai, Francois Rheault, Cailey I. Kerley, Katherine S. Aboud, Lori L. Beason-Held, Andrea T. Shafer, Susan M. Resnick, Lori C. Jordan, Adam W. Anderson, Kurt G. Schilling, and Bennett A. Landman Abstract Characterizing relationships between gray matter (GM) and white matter (WM) in early Alzheimer’s disease (AD) would improve understanding of how and...
Multimodal neuroimaging in pediatric type 1 diabetes: a pilot multisite feasibility study of acquisition quality, motion, and variability
Dec. 10, 2021—Leon Y. Cai, Costin Tanase, Adam W. Anderson, Karthik Ramadass, Francois Rheault, Chelsea A. Lee, Niral J. Patel, Sky Jones, Lauren M. LeStourgeon, Alix Mahon, Sumit Pruthi, Kriti Gwal, Arzu Ozturk, Hakmook Kang, Nicole Glaser, Simona Ghetti, Sarah S. Jaser, Lori C. Jordan, and Bennett A. Landman Abstract Type 1 diabetes (T1D) affects over 200,000...
MASiVar: Multisite, Multiscanner, and Multisubject Acquisitions for Studying Variability in Diffusion Weighted Magnetic Resonance Imaging
Aug. 30, 2021—Leon Y. Cai, Qi Yang, Praitayini Kanakaraj, Vishwesh Nath, Allen T. Newton, Heidi A. Edmonson, Jeffrey Luci, Benjamin N. Conrad, Gavin R. Price, Colin B. Hansen, Cailey I. Kerley, Karthik Ramadass, Fang-Cheng Yeh, Hakmook Kang, Eleftherios Garyfallidis, Maxime Descoteaux, Francois Rheault, Kurt G. Schilling, and Bennett A. Landman. MASiVar: Multisite, Multiscanner, and Multisubject Acquisitions for...
PreQual: An automated pipeline for integrated preprocessing and quality assurance of diffusion weighted MRI images
Jun. 23, 2021—Leon Y. Cai, Qi Yang, Colin B. Hansen, Vishwesh Nath, Karthik Ramadass, Graham W. Johnson, Benjamin N. Conrad, Brian D. Boyd, John P. Begnoche, Lori L. Beason-Held, Andrea T. Shafer, Susan M. Resnick, Warren D. Taylor, Gavin R. Price, Victoria L. Morgan, Baxter P. Rogers, Kurt G. Schilling, Bennett A. Landman. PreQual: An automated pipeline...
Joint cortical surface and structural connectivity analysis of Alzheimer’s Disease
Nov. 20, 2020—Leon Y. Cai, Cailey I. Kerley, Chang Yu, Katherine S. Aboud, Lori L. Beason-Held, Andrea T. Shafer, Susan M. Resnick, Lori C. Jordan, Adam W. Anderson, Kurt G. Schilling, Ilwoo Lyu, Bennett A. Landman. Joint cortical surface and structural connectivity analysis of Alzheimer’s Disease. SPIE Medical Imaging, 2021. Full Text: NIHMSID Abstract Joint independent component...