Diffusion microscopist simulator: a general Monte Carlo simulation system for diffusion magnetic resonance imaging

PLoS One. 2013 Oct 10;8(10):e76626. doi: 10.1371/journal.pone.0076626. eCollection 2013.


This article describes the development and application of an integrated, generalized, and efficient Monte Carlo simulation system for diffusion magnetic resonance imaging (dMRI), named Diffusion Microscopist Simulator (DMS). DMS comprises a random walk Monte Carlo simulator and an MR image synthesizer. The former has the capacity to perform large-scale simulations of Brownian dynamics in the virtual environments of neural tissues at various levels of complexity, and the latter is flexible enough to synthesize dMRI datasets from a variety of simulated MRI pulse sequences. The aims of DMS are to give insights into the link between the fundamental diffusion process in biological tissues and the features observed in dMRI, as well as to provide appropriate ground-truth information for the development, optimization, and validation of dMRI acquisition schemes for different applications. The validity, efficiency, and potential applications of DMS are evaluated through four benchmark experiments, including the simulated dMRI of white matter fibers, the multiple scattering diffusion imaging, the biophysical modeling of polar cell membranes, and the high angular resolution diffusion imaging and fiber tractography of complex fiber configurations. We expect that this novel software tool would be substantially advantageous to clarify the interrelationship between dMRI and the microscopic characteristics of brain tissues, and to advance the biophysical modeling and the dMRI methodologies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Membrane / metabolism
  • Diffusion Magnetic Resonance Imaging*
  • Humans
  • Monte Carlo Method*
  • Neurons / cytology
  • Software

Grant support

This research is partly supported by the National Science Council of Taiwan, the Partenariat Huber Currier Orchid project, the DFMRI and SimuDMRI projects approved by the French National Research Agency, and the European CONNECT project. CHY is grateful to the “Programme Joseph Fourier (2008–2010)” scholarship co-financed by the French Institute in Taipei, the CEA NeuroSpin Centre, and National Yang-Ming University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.