CIBC:Documentation:SCIRun:Reference:BioPSE

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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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