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Magnetic resonance imaging Category

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...

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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...

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3D UX-Net: A Large Kernel Volumetric ConvNet Modernizing Hierarchical Transformer for Medical Image Segmentation

Oct. 6, 2022—Ho Hin Lee, Shunxing Bao, Yuankai Huo, Bennett A. Landman, “3D UX-Net: A Large Kernel Volumetric ConvNet Modernizing Hierarchical Transformer for Medical Image Segmentation”, arXiv 2022 Full Text Abstract Vision transformers (ViTs) have quickly superseded convolutional networks (ConvNets) as the current state-of-the-art (SOTA) models for medical image segmentation. Hierarchical transformers (e.g., Swin Transformers) reintroduced several...

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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...

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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...

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TractEM: Evaluation of protocols for deterministic tractography white matter atlas

Dec. 3, 2021—Rheault, Francois, Roza G. Bayrak, Xuan Wang, Kurt G. Schilling, Jasmine M. Greer, Colin B. Hansen, Cailey Kerley et al. “TractEM: Evaluation of protocols for deterministic tractography white matter atlas.” Magnetic Resonance Imaging 85 (2022): 44-56. Full Text Abstract   Purpose: One of the key challenges of the manual delineation of white matter pathways is human-rater’s subjectivity in labeling....

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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...

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Automated, open-source segmentation of the Hippocampus and amygdala with the open Vanderbilt archive of the temporal lobe

Aug. 28, 2021—Plassard, Andrew J., Shunxing Bao*, Maureen McHugo, Lori Beason-Held, Jennifer U. Blackford, Stephan Heckers, and Bennett A. Landman. “Automated, open-source segmentation of the Hippocampus and amygdala with the open Vanderbilt archive of the temporal lobe.” Magnetic Resonance Imaging 81 (2021): 17-23. Full text: https://www.sciencedirect.com/science/article/abs/pii/S0730725X21000692 Abstract Examining volumetric differences of the amygdala and anterior-posterior regions of the...

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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...

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Generalizing deep whole-brain segmentation for post-contrast MRI with transfer learning

Dec. 26, 2020—Bermudez, C., Remedios, S. W., Ramadass, K., McHugo, M., Heckers, S., Huo, Y., & Landman, B. A. (2020). Generalizing deep whole-brain segmentation for post-contrast MRI with transfer learning. Journal of Medical Imaging, 7(6), 064004. Full Text: https://pubmed.ncbi.nlm.nih.gov/33381612/ Abstract Purpose: Generalizability is an important problem in deep neural networks, especially with variability of data acquisition in...

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