Reproducibility Category
Reproducibility evaluation of the effects of MRI defacing on brain segmentation
Nov. 10, 2023—Chenyu Gao, Bennett A. Landman, Jerry L. Prince, Aaron Carass. “Reproducibility evaluation of the effects of MRI defacing on brain segmentation”. J. Med. Imag. 10(6), 064001 (2023), https://doi.org/10.1117/1.JMI.10.6.064001, [PDF] Abstract Purpose Recent advances in magnetic resonance (MR) scanner quality and the rapidly improving nature of facial recognition software have necessitated the introduction of MR defacing...
Characterizing Streamline Count Invariant Graph Measures of Structural Connectomes
Sep. 6, 2023—Nancy R. Newlin, Francois Rheault, Kurt G. Schilling, Bennett A. Landman. “Characterizing Streamline Count Invariant Graph Measures of Structural Connectomes” Journal of Magnetic Resonance Imaging. January 2023. Full Text Background While graph measures are used increasingly to characterize human connectomes, uncertainty remains in how to use these metrics in a quantitative and reproducible manner. Specifically, there is...
Distortion correction of functional MRI without reverse phase encoding scans or field maps
Aug. 31, 2023—Tian Yu, Leon Y. Cai, Salvatore Torrisi, An Thanh Vu, Victoria L. Morgan, Sarah E. Goodale, Karthik Ramadass, Steven L. Meisler, Jinglei Lv, Aaron E.L. Warren, Dario J. Englot, Laurie Cutting, Catie Chang, John C. Gore, Bennett A. Landman, Kurt G. Schilling Paper: https://www.sciencedirect.com/science/article/pii/S0730725X23001121 Code: https://github.com/MASILab/SynBOLD-DisCo Abstract Functional magnetic resonance images (fMRI) acquired using echo planar sequences...
Inpainting Missing Tissue in Multiplexed Immunofluorescence Imaging
Dec. 10, 2021—Shunxing Bao, Yucheng Tang, Ho Hin Lee, Riqiang Gao, Qi Yang, Xin Yu, Sophie Chiron, Lori A. Coburn, Keith T. Wilson, Joseph T. Roland, Bennett A. Landman, Yuankai Huo. “Inpainting Missing Tissue in Multiplexed Immunofluorescence Imaging” Medical Imaging 2022: Digital and Computational Pathology. International Society for Optics and Photonics, accepted Full text: [TBD] Abstract Multiplex immunofluorescence (MxIF) is...
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....
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...
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...
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...
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...
Enabling Multi-shell b-Value Generalizability of Data-Driven Diffusion Models with Deep SHORE
Jan. 17, 2020—Nath V, Lyu I, Schilling KG, Parvathaneni P, Hansen CB, Huo Y, Janve VA, Gao Y, Stepniewska I, Anderson AW, Landman BA. Enabling Multi-shell b-Value Generalizability of Data-Driven Diffusion Models with Deep SHORE. In International Conference on Medical Image Computing and Computer-Assisted Intervention 2019 Oct 13 (pp. 573-581). Springer, Cham. Full text: https://arxiv.org/ftp/arxiv/papers/1907/1907.06319.pdf Abstract Intra-voxel...