Hong-Hsi Lee1, Els Fieremans2, Dmitry S Novikov2. 1. Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA. Electronic address: Honghsi.Lee@nyulangone.org. 2. Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, NY, USA; Center for Advanced Imaging Innovation and Research (CAI2R), New York University School of Medicine, New York, NY, USA.
Abstract
BACKGROUND: Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. NEW METHOD: Here we describe the details of implementing Monte Carlo simulations in three-dimensional (3d) voxelized segmentations of cells in microscopy images. Using the concept of the corner reflector, we largely reduce the computational load of simulating diffusion within and exchange between multiple cells. Precision is further achieved by GPU-based parallel computations. RESULTS: Our simulation of diffusion in white matter axons segmented from a mouse brain demonstrates its value in validating biophysical models. Furthermore, we provide the theoretical background for implementing a discretized diffusion process, and consider the finite-step effects of the particle-membrane reflection and permeation events, needed for efficient simulation of interactions with irregular boundaries, spatially variable diffusion coefficient, and exchange. COMPARISON WITH EXISTING METHODS: To our knowledge, this is the first Monte Carlo pipeline for MR signal simulations in a substrate composed of numerous realistic cells, accounting for their permeable and irregularly-shaped membranes. CONCLUSIONS: The proposed RMS pipeline makes it possible to achieve fast and accurate simulations of diffusion in realistic tissue microgeometry, as well as the interplay with other MR contrasts. Presently, RMS focuses on simulations of diffusion, exchange, and T1 and T2 NMR relaxation in static tissues, with a possibility to straightforwardly account for susceptibility-induced T2* effects and flow.
BACKGROUND: Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. NEW METHOD: Here we describe the details of implementing Monte Carlo simulations in three-dimensional (3d) voxelized segmentations of cells in microscopy images. Using the concept of the corner reflector, we largely reduce the computational load of simulating diffusion within and exchange between multiple cells. Precision is further achieved by GPU-based parallel computations. RESULTS: Our simulation of diffusion in white matter axons segmented from a mouse brain demonstrates its value in validating biophysical models. Furthermore, we provide the theoretical background for implementing a discretized diffusion process, and consider the finite-step effects of the particle-membrane reflection and permeation events, needed for efficient simulation of interactions with irregular boundaries, spatially variable diffusion coefficient, and exchange. COMPARISON WITH EXISTING METHODS: To our knowledge, this is the first Monte Carlo pipeline for MR signal simulations in a substrate composed of numerous realistic cells, accounting for their permeable and irregularly-shaped membranes. CONCLUSIONS: The proposed RMS pipeline makes it possible to achieve fast and accurate simulations of diffusion in realistic tissue microgeometry, as well as the interplay with other MR contrasts. Presently, RMS focuses on simulations of diffusion, exchange, and T1 and T2 NMR relaxation in static tissues, with a possibility to straightforwardly account for susceptibility-induced T2* effects and flow.
Authors: Els Fieremans; Yves De Deene; Steven Delputte; Mahir S Ozdemir; Yves D'Asseler; Jelle Vlassenbroeck; Karel Deblaere; Eric Achten; Ignace Lemahieu Journal: J Magn Reson Date: 2007-11-01 Impact factor: 2.229
Authors: Susie Y Huang; Thomas Witzel; Boris Keil; Alina Scholz; Mathias Davids; Peter Dietz; Elmar Rummert; Rebecca Ramb; John E Kirsch; Anastasia Yendiki; Qiuyun Fan; Qiyuan Tian; Gabriel Ramos-Llordén; Hong-Hsi Lee; Aapo Nummenmaa; Berkin Bilgic; Kawin Setsompop; Fuyixue Wang; Alexandru V Avram; Michal Komlosh; Dan Benjamini; Kulam Najmudeen Magdoom; Sudhir Pathak; Walter Schneider; Dmitry S Novikov; Els Fieremans; Slimane Tounekti; Choukri Mekkaoui; Jean Augustinack; Daniel Berger; Alexander Shapson-Coe; Jeff Lichtman; Peter J Basser; Lawrence L Wald; Bruce R Rosen Journal: Neuroimage Date: 2021-08-28 Impact factor: 7.400
Authors: Davood Karimi; Lana Vasung; Camilo Jaimes; Fedel Machado-Rivas; Shadab Khan; Simon K Warfield; Ali Gholipour Journal: Med Image Anal Date: 2021-06-03 Impact factor: 13.828