Modeling and Visualization of Models in SCIRun/BioPSE

From NCRR Biomedical Software Development, Engineering, and Dissemination Wiki

Status of Subproject

In Process

FEM Modeling of Electric Fields in Models

SCIRun and BioPSE are powerful tools for finite element modeling of electric fields in image based models. An introduction and tutorial for these programs and the concepts behind them are available here. The module referenceis also very helpful in understanding the functionality of networks which were created by other people as well as developing your own. The following information is meant as an introduction to the steps needed to model and visualize electric fields in the models created in 3D Slicer. The specifics of functional nets will eventually be described in example based tutorials.

Meshing

SCIRun can take the voxels represented in the NRRD file and convert them into a tetrahedral mesh optimal for iterative computation and visualization in the SCIRun environment. The specifics of this vary depending on the application. The meshing capabilities within both SCIRun and 3D Slicer are an active area of research.

Assigning Conductivities

The values for conductivities and related quantities for various biological tissues are available in the literature. Appropriate values should be assigned to each tissue type. There is wide variation and care should be taken in choosing them. These can then be entered within an appropriate net using the Modify Conductivity Module. Values can either be entered into the GUI or defined by an Nx9 matrix.

Solving the Volume Conductor Problem

Once a model has been created and apporopriate conductivities have been assigned to the tissues a net must be created to solve the volume conductor problem and visualize the result. The basic theory and steps to solve the problem for the case of a simple dipole are summarized Chapters 5-7 of the SCIRun Tutorial.

Inserting Arbitrarily Shaped Electrodes into the Model

We are interested in solving the forward problem not for a simple dipole but for an electric field created by internal inplantable defibrillator electrodes inserted in different positions in image based models of children. It involves taking the models created in the previous steps in the pipeline and inserting appropriately shaped electrodes into anatomically realistic positions. In order to do this the previously created mesh must be "remeshed" to remove the original "tissue" elements and replace them with "electrode" elements in which the voltage can be set. The technology to do this is currently being developed as explained here.

Functional Example Net as a Tutorial

Scalable nets for modeling the volume conductor problem and visualization of models created in 3D Slicer are being developed.

Subproject Requirements

Control Structure

• Being defined and built from within SCI

Algorithms

• Smoothing/Premeshing optimization
• Meshing- Explore optimal meshing strategy/algorithms for process. Utilize existing SCIRun meshing or outside product.
• FE stiffness matrix- Utilize existing modules in BioPSE
• Insert electrodes module- This will require local remeshing and rebuilding of components of SCIRun.

Data Representation/User Interface

• Visualization of torso
  • Allow ability to move electrodes in torso with precision within torso

• Visualization of torso surface field
  • Show surface potentials on the chest in separate window

• Visualization of Heart
  • Visualization of voltage gradients in heart
  • Visualization of electrodes relative to heart

• Measurement of voltage field within heart
  • Histogram
  • Widget with ability to sample within visualization

--MJ 09:57, 25 Jan 2006 (MST)