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User Friendly, Fast and Robust Monte Carlo Diffusion and Collision Simulator
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• Introduction
• Quick start
• Status
• Simulations
• Bugs and feature requests
• Documentation
• Versioning
• Developers
• Copyright and license

The Monte Carlo Diffusion and Collision simulator (MC/DC), is an C++ open source Diffusion Weighted Magnetic Resonance Imaging (DW-MRI) Monte Carlo Simulator. For a in-detail explanation of the numerical framework and basics on DW-MRI imaging we refer the visitor to the following publication: https://doi.org/10.3389/fninf.2020.00008

AUTHOR=Rafael-Patino Jonathan, Romascano David, Ramirez-Manzanares Alonso, Canales-Rodríguez Erick Jorge, Girard Gabriel, Thiran Jean-Philippe TITLE=Robust Monte-Carlo Simulations in Diffusion-MRI: Effect of the Substrate Complexity and Parameter Choice on the Reproducibility of Results
JOURNAL=Frontiers in Neuroinformatics
VOLUME=14 YEAR=2020 PAGES=8
URL=https://www.frontiersin.org/article/10.3389/fninf.2020.00008
DOI=10.3389/fninf.2020.00008 ISSN=1662-5196

Several quick start options are available:

• Download a pre-compiled version if available
• Compile the sources
• Read the Getting started page for information on the basic parameters needed.
• Tutorial: Simulation in free diffusion
• Tutorial: Simulation in gamma distributed cylinders
• Tutorial: Simulation in PLY models

The MC/DC Simulator only uses C++ Eigen template library for linear algebra as an external dependency, which is included in the repository; all other basic structures ---from 3d-mesh-models handling to the MRI signal synthesis---are built from scratch in the following hierarchical structure.

All the displayed components depicted above are organized in separated class-oriented modules with abstract-based prototypes that can inherited and re-implemented to augment the functionality and scope of the a simulations.

Have a bug or a feature request? Please first read the ongoing development chart and search for existing and closed issues. If your problem or idea is not addressed yet, please open a new issue.

The MC/DC technical documentation is automatically generated using doxygen and the source-files comments, and can be found in here in html format, or in here as a .tex source file.

For full reproducibility of the results presented on: https://www.frontiersin.org/articles/10.3389/fninf.2020.00008/full, the first version, 1.42, is the same version released in the paper's GitHub repository: https://github.com/jonhrafe/Robust-Monte-Carlo-Simulations.

However, future releases may not follow the conf_file conventions used and included in the aforementioned repository.

Jonathan Rafael-Patino

• https://people.epfl.ch/jonathan.patinolopez?lang=en
• https://www.linkedin.com/in/jonhrafe/

GNU Lesser General Public License v2.1

Primarily used for software libraries, the GNU LGPL requires that derived works be licensed under the same license, but works that only link to it do not fall under this restriction.