Single Slice Thigh CT Muscle Group Segmentation with Domain Adaptation and Self-Training
Aug. 31, 2023—Qi Yang, Xin Yu, Ho Hin Lee, Leon Y. Cai, Kaiwen Xu, Shunxing Bao, Yuankai Huo , Ann Zenobia Moore, Sokratis Makrogiannis, Luigi Ferrucci, Bennett A. Landman. Objective: Thigh muscle group segmentation is important for assessment of muscle anatomy, metabolic disease and aging. Many efforts have been put into quantifying muscle tissues with magnetic resonance...
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...
Anomalous and heterogeneous characteristics of the BOLD hemodynamic response function in white matter
Dec. 13, 2022—Kurt G Schilling, Muwei Li, Francois Rheault, Zhaohua Ding, Adam W Anderson, Hakmook Kang, Bennett A Landman, John C Gore. “Anomalous and heterogeneous characteristics of the BOLD hemodynamic response function in white matter”. Cerebral Cortex Communications 3 (3), tgac035 (2022). Full Text Abstract Detailed knowledge of the BOLD hemodynamic response function (HRF) is crucial for accurate...
Minimal number of sampling directions for robust measures of the spherical mean diffusion weighted signal: effects of sampling directions, b-value, signal-to-noise ratio, hardware, and fitting strategy
Dec. 13, 2022—Kurt G Schilling, Marco Palombo, Kristin P. O’Grady, Anna J.E. Combes, Adam W Anderson, Bennett A Landman, Seth A Smith. “Minimal number of sampling directions for robust measures of the spherical mean diffusion weighted signal: effects of sampling directions, b-value, signal-to-noise ratio, hardware, and fitting strategy”. Magnetic Resonance Imaging 94, 25-35 (2022). Full Text Abstract...
Aging and white matter microstructure and macrostructure: a longitudinal multi-site diffusion MRI study of 1218 participants
Dec. 13, 2022—Kurt G Schilling, Derek Archer, Fang-Cheng Yeh, Francois Rheault, Leon Cai, Colin Hansen, Qi Yang, Karthik Ramdass, Andrea Shafer, Susan Resnick, Kimberly R. Pechman, Katherine A. Gifford, Timothy J. Hohman, Angela Jefferson, Adam W Anderson, Hakmook Kang, Bennett A Landman. “Aging and white matter microstructure and macrostructure: a longitudinal multi-site diffusion MRI study of 1218 participants.” Brain...
Prevalence of white matter pathways coming into a single diffusion MRI voxel orientation: the bottleneck issue in tractography
Dec. 13, 2022—Kurt G. Schilling, Chantal M.W. Tax, Francois Rheault, Bennett Landman, Adam Anderson, Maxime Descoteaux*, Laurent Petit*. “Prevalence of white matter pathways coming into a single diffusion MRI voxel orientation: the bottleneck issue in tractography”. Human Brain Mapping 43(4), 1196-1213. (2022) Full Text Abstract Characterizing and understanding the limitations of diffusion MRI fiber tractography is a...
Tractography dissection variability: what happens when 42 groups dissect 14 white matter bundles on the same dataset?
Dec. 13, 2022—Kurt G Schilling, Francois Rheault, Laurent Petit, Colin B Hansen, Vishwesh Nath, Fang-Cheng Yeh, Gabriel Girard, Muhamed Barakovic, Jonathan Rafael-Patino, Thomas Yu, Elda Fischi-Gomez, Marco Pizzolato, Riccardo Galbusera, Mario Ocampo-Pineda, Simona Schiavi, Erick J Canales-Rodriguez, Alessandro Daducci, Cristina Granziera, Giorgio Innocenti, Jean-Philippe Thiran, Laura Mancini, Stephen Wastling, Sirio Cocozza, Maria Petracca, Giuseppe Pontillo, Matteo Mancini,...
Fiber tractography bundle segmentation depends on scanner effects, acquisition, diffusion sensitization, and bundle segmentation workflow
Dec. 13, 2022—Kurt G Schilling, Chantal MW Tax, Francois Rheault, Colin B Hansen, Qi Yang, Fang-Cheng Yeh, Leon Y Cai, Adam W Anderson, Bennett A Landman “Fiber tractography bundle segmentation depends on scanner effects, acquisition, diffusion sensitization, and bundle segmentation workflow”. NeuroImage. 242, 118451 (2021). Full Text Abstract When investigating connectivity and microstructure of white matter pathways...
On the generalizability of diffusion MRI signal representations across acquisition parameters, sequences and tissue types: chronicles of the MEMENTO challenge
Dec. 13, 2022—Alberto De Luca, Andrada Ianus, Alexander Leemans, Marco Palombo, Noam Shemesh, Hui Zhang, Daniel C Alexander, Markus Nilsson, Martijn Froeling, Geert-Jan Biessels, Mauro Zucchelli, Matteo Frigo, Enes Albay, Sara Sedlar, Abib Alimi, Samuel Deslauriers-Gauthier, Rachid Deriche, Rutger Fick, Maryam Afzali, Tomasz Pieciak, Fabian Bogusz, Santiago Aja-Fernandez, Evren Ozarslan, Derek K Jones, Haoze Chan, Mingwu Jin,...