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MRI2FE

Patient-specific Finite Element Model Generation from medical imaging data

Introduction

This package provides workflows for the generation of finite element (FE) models of the human head from patient-specific magnetic resonance imaging (MRI) and magnetic resonance elastography (MRE) data. The objective of this toolkit is to provide fast and accurate generation of finite element head models (FEHMs) for a variety of physics and multi-physics analyses. This package leverages industry standard tools including Advanced Normalization Tools (ANTs) for MRI transformation and segmentation 12, and the Computational Geometry Algorithms Library (CGAL) for meshing 34.

Installation

Installing from wheel

To install the package, download the appropriate wheel file from the most recent release, and then install on your local machine


pip install ./name-of-wheel.whl

Installing from source

To install the package from source, download or clone the repository to your local machine. Run the appropriate installation script for your system, which will install all dependencies as well as the package.

git clone https://github.com/turnerjennings/MRI2FE

cd MRI2FE

#if on windows
./install_windows.bat

#if on mac
./install_mac.sh

#if on linux
./install_linux.sh

On Windows, after installation from source you may run into an error stating "DLL load failed". This issue occurs intermittently on Windows and is due to the dependencies for the CGAL library not linking correctly. To address the issue, try reinstalling. If the issue persists, find the location of the DLLs "gmp-10.dll" and "mpfr6.dll" in the ./vcpkg directory and copy them to the installation location.

On Windows, there is an intermittent issue during installation where certain boost libraries cannot be located. Re-running the installation consistently fixes this issue.

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  2. Arno Klein, Jesper Andersson, Babak A. Ardekani, John Ashburner, Brian Avants, Ming-Chang Chiang, Gary E. Christensen, D. Louis Collins, James Gee, Pierre Hellier, Joo Hyun Song, Mark Jenkinson, Claude Lepage, Daniel Rueckert, Paul Thompson, Tom Vercauteren, Roger P. Woods, J. John Mann, and Ramin V. Parsey. Evaluation of 14 nonlinear deformation algorithms applied to human brain mri registration. NeuroImage, 46(3):786–802, 2009. URL: https://www.sciencedirect.com/science/article/pii/S1053811908012974, doi:https://doi.org/10.1016/j.neuroimage.2008.12.037. ↩

  3. The CGAL Project. CGAL User and Reference Manual. CGAL Editorial Board, 6.0.1 edition, 2024. URL: https://doc.cgal.org/6.0.1/Manual/packages.html. ↩

  4. Pierre Alliez, Clément Jamin, Laurent Rineau, Stéphane Tayeb, Jane Tournois, and Mariette Yvinec. 3D mesh generation. In CGAL User and Reference Manual. CGAL Editorial Board, 6.0.1 edition, 2024. URL: https://doc.cgal.org/6.0.1/Manual/packages.html#PkgMesh3. ↩