Scientific Training III

Statistical Shape Modelling and Simulation of Deformable Models for Biomechanics

PhD course on continuum based modeling and solving using finite element method with example tools such as FEniCS & SOFA. Also statistical shape models are covered to describe variance in for geometry of a population.

Course content

Simulation is a valuable tool when working with biomechanical modeling of humans as it allows for analysis or prediction for either scenarios that would be too invasive or high risk to conduct on real human experiments or to fill in the gaps where only sparse knowledge or data is accessible. On the other hand data-driven approaches and statistical analysis of larger populations have similar shown to be extremely powerful in understanding the nature of how things work or more precisely how the sensitivity of different factors influence each other. The two approaches: simulation and statistical analysis are not necessarily disjoint given one is model driven and the other data-driven. In this course we peel of the first layer in combining these two approaches in the context of biomechanical modeling of humans.

In this course we will focus on how to bridge the gap between data and simulation of deformable models. The courses addresses fundamental background and terminology in simulation of deformable models with multiple practical examples. Participants will learn to use state of the art simulation tools such as FEniCs, Sofa and possible other tools as well. Having formed a strong basis for continuum mechanics and simulations the course tries to connect simulation as a tool to statistical analysis. How can we use data for analysis and how can simulation results be processed by analysis to conclude hypotheses on larger populations.

The course aims at combining basic knowledge and skills in two different disciplines into one common frame. The intended audience is PhDs in computer science who does not necessarily have a strong background in both these fields.

ECTS credits

3 ECTS points.

Learning objectives:

i) Describe shapes, shape spaces, and shape variability in the context of template shapes deformed by the action of deformations of the shape domain.

ii) Perform statistical analysis and computations on simple shape spaces.

iii) Apply statistical analysis to large scale simulation studies

iv) Account for common challenges in biomechanical modeling, describe how to cope without a gold standard, validation and verification.

v) Derive basic definitions of stress and strain tensors and apply these to compute stress/strain measures given known displacement fields

vi) Describe what plasticity, viscosity, yield point, yield strength, tensile limit etc and identify these concepts correctly if given for instance a stress-strain curve

vii) Explain the governing equations of motion for hyper elastic material simulation and run simulations using different constitutive equations in for instance FEniCS or FEBio

viii) Present visualizations of simulation results such as von Misses or Tresca stress or similar and reason about the meaning of high and low values (yield values)

ix) Describe how to use multi-model simulation with contact in SOFA

x) Setup and run a simple SOFA simulation with deformable and rigid bodies in contact.

Systems and software prerequisites

To participate in the course, participants need to bring own laptops with Google Chrome installed.

Syllabus and course material

Syllabus will be forwarded to all participants after the registration deadline. Course material is available in Internal Forum > courses > material-t3  (section accessed only by project members)

Preliminary program

Final program and detailed speaker presentation to be announced.

Speakers