Software - Igor Peterlik

Simulation Open Framework Architecture (SOFA) is an open-source software

dedicated to research in medical simulation and also used to develop new training technologies.

I've been contributing to SOFA since November 2009. If you want to learn more about SOFA, see the YouTube channel.

Besides the contributions to the framework, I am also an author of several SOFA plugins hosted at Inria GitLAB. If you are interested in any of those plugins, contact me via my e-mail address.

Selection of plugins:

Optimus: a SOFA plugin for stochastic real-time simulation (work in progress). Details available in publication Towards an efficient data assimilation in physically-based medical simulations (BIBM 2015) and application recently published in Image-driven Stochastic Identification of Boundary Conditions for Predictive Simulation (MICCAI 2015). Currently being developed towards integrating methods of machine learning.
BezierSkeletonization: a SOFA plugin for extraction of center lines from segmented images of vascularizations. Details available in a publication Robust Automatic Graph-based Skeletonization of Hepatic Vascular Trees (CVII-Stent 2017).
ImageWarping: a SOFA plugin for advanced warping of 3D medical images from deformed meshes, employing the radial-basis interpolation. Details available in a publication: Fast reconstruction of image deformation field using radial basis function (ISBI 2017).
Pardiso@SOFA: a plugin allowing to use Pardiso solver in SOFA. It also contains an accelerated resolution of constraints based on partial factorization (see a demo video).
SofaValidation: tools for a systematic validation of SOFA (work in progress).
SofaVascularToolking: tools for extraction and registration of vascular and vascularized structures (work in progress).

MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth

generation programming language.

I have developed a FEM package MatFleX implemented exclusively in Matlab. The modeling package contains:

Finite element formulation of StVenant-Kirchhoff and 2-coefficient Mooney-Rivlin hyperelastic materials over
a 3D mesh composed of linear tetrahedra.
Implementation of both materials available in total Lagrangian and updated Lagrangian formulations.
Static and quasi-static simulation allowing for defining applied body forces, surface pressure,
surface tractions and prescribed displacements (heterogeneous Dirichlet boundary conditions).
Implementation of Dirichlet conditions using Lagrange multipliers, allowing for extraction of applied forces.
Simulation of contacts with a rigid obstacle (currently limited to a plane) based on Linear Complementarity Problem.
Import/export using VTK and CSV files. Allows for using with Paraview for interactive creation of geometry and visualization.
Matlab fast visualization of simulation results.
Verification and benchmark scripts comparing the simulation to results obtained by FeBIO.

MatFleX works with Matlab versions 8.2 -- 9.2.

Documentation of MatFleX is available here.