# CIBC:Documentation:SCIRun:Reference:BioPSE

From SCIRun Documentation Wiki

## Contents

**BioPSE Reference**

**Package Description**

**Module Reference**

**DataIO**

- ImportDenseMatrixFromRaw
- The RawtoDenseMatrix mdoule reads CVRTI potentials, with output as a DenseMatrix.

**Forward**

- ApplyFEMCurrentSource
- The ApplyFEMCurrentSource module builds the right-hand side (ColumnMatrix) to reflect monopolar and dipolar current sources for finite-element based bioelectric field problems.

- ApplyFEMElectrodeSource
- Due to course current dipoles, the ApplyFEMElectrodeSource module changes and recreates the right-hand side (RHS) for the Finite Elements discretization approach.

- ApplyFEMVoltageSource
- The module changes/creates the right-hand side (RHS) and forward matrices for voltgage (Dirichlet) boundary conditions.

- BuildBEMSrcToInfTransferMatrix
- This module builds the electric potential distribution on a closed surface arising from a dipole distribution contained within the surface.

- BuildBEMatrix
- The module solves a discretized model of Laplace's equation in a 3D volume conductor model using "surface method", given a particular type of boundary condition.

- BuildEITMatrix
**Deprecated in SCIRun 4.7.**The module solves a discretized model of Laplace's equation in a 3D volume conductor model using "surface method", given a particular type of boundary condition.

- BuildFEMatrix
- The module sets up a mesh with conductivity tensors for bioelectric field problems.

- CalcTMP
- Calculates the transmembrane action potentials given the input parameters generated from ECGSim.

- CalculateCurrentDensity
- Compute the current density vector field

- ConvertFieldDataFromIndicesToTensors
- Change a Field of ints, into a Field of Tensors.

- ConvertFieldDataFromTensorsToIndices
- Change a Field of ints, into a Field of Tensors.

- CreateAnisoSphereParameters
**Deprecated.**CreateAnisoSphereParameters implements a four-layer anisotropic spherical volume conductor.

- CreateDiscreteAnisoSpheres
**Deprecated.**Scale the geometry of a sphere to a requested size and assign a conductivity tensor to each cell.

- CreateElectrodeParameterMatrices
- This modules generates EIT electrode information for 2D models as two vectors containing electrode parameter values.

- CreateTrigCurrentPattern
- Generates a trigonometric current pattern for EIT testing.

- GetActivationTimes
- Accepts a matrix of potentials on a surface and calculates the activation times by selecting the lowest (most negative) derivative.

- InsertElectrodes
- Insert electrodes into a finite element mesh.

- InsertVoltageSource
- Insert electrodes into a finite element mesh.

- IntegrateCurrent
- Compute the current across a surface.

- SetEITGround
**Deprecated in SCIRun 4.7.**The module performs an average reference.

- SetWireElectrodePotential
- Configure an electrode.

- SetWireElectrodeProperties
- Configure an electrode.

- SimulateDipoleInAnisoSpheresAnalytically
**Deprecated.**Due to a specified dipole, the potential on the outer sphere of a four layer spherical volume conductor is computed.

- SimulateDipoleInSphereAnalytically
**Deprecated.**Due to the specified dipoles, the SimulateDipoleInSphereAnalytically module fills the sphere field with potentials values.

- SimulateEITAnalytically
**Deprecated in SCIRun 4.7.**The module computes a forward solution for the electrical impedance tomography problem in 2D.

- SimulateForwardMagneticField
- Calculation of magnetic field at given detector points due to specificed dipoles.

**Inverse**

- BuildSurfaceLaplacianMatrix
- Transform attributes

- OptimizeConductivities
- This module optimizes (estimates) electrical conductivities for a given finite element mesh.

- OptimizeDipole
- Summary not available yet.

- SolveInverseProblemWithTSVD
- Solve inverse problem using Truncated SVD.

- SolveInverseProblemWithTikhonov
- This module applies SolveInverseProblemWithTikhonov regularization to an existing forward model, with flexible control of regularization type and parameters. Currently, the module solves the inverse problem in a single time-instant. This module requires a forward model matrix, geometries for the associated surfaces, and some remote boundary conditions, i.e., torso or head surface potentials.

- SolveInverseProblemWithTikhonovSVD
- Solve inverse problem using Tikhonov regularization by using SVD.

**LeadField**

- BuildElemLeadField
- Summary not available yet.

- BuildLeadFieldSourcesFromElectricCurrentMatrix
**Deprecated.**Assign data to a field.

- CalculateMisfitField
- Summary not available yet.

**Modeling**

- AbsorbSegFieldIslands
**Deprecated.**Create and process a segmented volume: erosion/dilation/open/close/absorb.

- ConvertSegFieldToLatVol
**Deprecated.**Create a LatVolField from a SegLatVolField -- choose a quantity to store as the data.

- ConvertSegFieldToSepSurfs
**Deprecated.**Create Separating surfaces from a SegLatVolField.

- ConvertSepSurfToQuadSurf
**Deprecated.**Change the Separating Surface into a QuadSurf.

- GetSingleSurfaceFromSepSurfs
**Deprecated.**Extract a single QuadSurf (one connected component) from a Separating Surface.

- SetConductivities
- Change the conductivity tensors in a field.

**NeuroFEM**

- InterfaceWithNeuroFEMForward
- Invoke the NeuroFEM ipm program to solve the forward problem for the inputs.

- InterfaceWithNeuroFEMInverse
- Invoke the NeuroFEM ipm program to solve the input problem for the inputs.

**Visualization**

- ShowAndEditDipoles
- Summary not available yet.

- ViewLeadSignals
- The ViewLeadSignals module graphs a Matrix that has rows of potentials.

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