SIMBIO/Designreport/Appendix A

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Contents

List of methods and parameters of user interface I

Inverse methods:

Linear Estimation
uif1_linear_estimation_oncortex( inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, inForwardType, inInverseType, inInverterType)
uif1_linear_estimation_onbrainsurface(inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, inForwardType, inInverseType inInverterType)
uif1_linear_estimation_inbrainvolume(inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, inForwardType, inInverseType, inInverterType)
Non-Linear Estimation
uif1_non_linear_estimation_oncortex(inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, inForwardType, inNonLinearInverseType, inInverterType)
uif1_non_linear_estimation_ onbrainsurface (inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, inForwardType, inNonLinearInverseType, inInverterType)
uif1_non_linear_estimation_ inbrainvolume (inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, inForwardType, inNonLinearInverseType, inInverterType)
Goal Function Scan
uif1_goalfunctionscan_oncortex(inReferenceData, inMRI, inSensorConfiguration, inSensorType,
outResult, inForwardType)
uif1_goalfunctionscan_onbrainsurface(inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, inForwardType)
uif1_goalfunctionscan_inbrainvolume(inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, inForwardType)
Music
uif1_MUSIC_oncortex(inReferenceData, inMRI, inSensorConfiguration, inSensorType,
outResult, inForwardType)
uif1_MUSIC_onbrainsurface(inReferenceData, inMRI, inSensorConfiguration, inSensorType,
outResult, inForwardType);
uif1_MUSIC_inbrainvolume(inReferenceData, inMRI, inSensorConfiguration, inSensorType,
outResult, inForwardType )
Discrete Dipole Fit
uif1_discrete_dipole_fit_oncortex(inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, nDipoles, inForwardType)
uif1_discrete_dipole_fit_ onbrainsurface (inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, nDipoles, inForwardType)
uif1_discrete_dipole_fit_ inbrainvolume (inReferenceData, inMRI, inSensorConfiguration,
inSensorType, outResult, nDipoles, inForwardType)
Dipole Fit
uif1_movingdipolfit(inReferenceData, inMRI, inSensorConfiguration, inSensorType, outResult,
nDipoles, inForwardType, inOptimizerType, inCriteriaType, inInverterType
inSearchVolumeType, inIntialGuessType)
uif1_rotatingdipolfit(inReferenceData, inMRI, inSensorConfiguration, inSensorType, outResult,
nDipoles, inForwardType, inOptimizerType, inCriteriaType, inInverterType
inSearchVolumeType, inIntialGuessType)
uif1_fixeddipolfit(inReferenceData, inMRI, inSensorConfiguration, inSensorType, outResult,
nDipoles, inForwardType, inOptimizerType, inCriteriaType, inInverterType
inSearchVolumeType, inIntialGuessType)

All methods return a boolean value, indicating either a successful execution or a failure.

Parameters I

Parameter Type Description
inReferenceData utMatrix_t<double> Matrix containing the reference data
inMRI MRItype class containing the mri
inSensorConfiguration SensorConfiguration class containing the description of the sensor configuration
inSensorType sensortype_e

{sensortype_EEG, sensortype_MEG}

type of sensors: EEG, MEG
outResult utMatrix_t<double> Matrix containing the result
nDipoles int Number of dipoles for dipole fit

Parameters II (switches)

Parameter Possible Values Default
inForwardType forwardtype_Sphere

forwardtype_BEM

forwardtype_FEM

forwardtype_BEM
inInverseType linearinversetype_L2

linearinversetype_Loreta

linearinversetype_ContinuousL2

linearinversetype_ContinuousL2-Gradient

linearinversetype_L2
inNonLinearInverse-Typenonlinearinversetype_L1 nonlinearinversetype_L1
inInverterType

invertertype_Tikhonow,

invertertype_TruncatedSVD

invertertype_TruncatedSVD
inOptimizerType

optimizertype_SimplexOptimizer

optimizertype_MarquardtOptimizer

optimizertype_SimulatedAnnealing

optimizertype_Marquardt

Optimizer

inCriteriaType

criteriatype_MinimumSquareError

criteriatype_MaximumEntropy

criteriatype_MaximumProbability

criteriatype_MinimumSquare

Error

inSearchVolumeType searchvolumetype_InEntireBrain searchvolumetype_InEntireBrain
inIntialGuessType intialguesstype_Standard intialguesstype_Standard

List of methods and parameters of user interface II

Inverse Methods:

Linear Estimation
uif2_linear_estimation_oncortex(inReferenceDataFileName, inCortexGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType,
inInverseType, inInverterType)
uif2_linear_estimation_onbrainsurface(inReferenceDataFileName, inBrainSurfaceGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType,
inInverseType, inInverterType)
uif2_linear_estimation_inbrainvolume(inReferenceDataFileName, inBrainVolumeGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType,
inInverseType, inInverterType)
Non-Linear Estimation
uif2_non_linear_estimation_oncortex(inReferenceDataFileName, inCortexGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType
inNonLinearInverseType, inInverterType)
uif2_non_linear_estimation_onbrainsurface(inReferenceDataFileName, inCortexGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType,
inNonLinearInverseType, inInverterType)
uif2_non_linear_estimation_ inbrainvolume (inReferenceDataFileName, inCortexGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType,
inNonLinearInverseType, inInverterType)
Goal Function Scan
uif2_goalfunctionscan_oncortex(inReferenceDataFileName, inCortexGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType)
uif2_goalfunctionscan_onbrainsurface(inReferenceDataFileName, inBrainSurfaceGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType)
uif2_goalfunctionscan_inbrainvolume(inReferenceDataFileName, inBrainVolumeGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType)
Music
uif2_MUSIC_oncortex (inReferenceDataFileName, inCortexGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType)
uif2_MUSIC_onbrainsurface(inReferenceDataFileName, inBrainSurfaceGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType)
uif2_MUSIC_inbrainvolume(inReferenceDataFileName, inBrainVolumeGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, inForwardType)
Discrete Dipole Fit
uif2_discrete_dipole_fit_oncortex(inReferenceDataFileName, inCortexGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, nDipoles,
inForwardType)
uif2_discrete_dipole_fit_onbrainsurface(inReferenceDataFileName, inCortexGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, nDipoles,
inForwardType)
uif2_discrete_dipole_fit_ inbrainvolume(inReferenceDataFileName, inCortexGridFileName,
inHeadGridFileName, inSensorConfigurationFileName, outResultFilename, nDipoles,
inForwardType)
Dipole Fit
uif2_movingdipolfit(inReferenceDataFileName, inHeadGridFileName,
inSensorConfigurationFileName, outResultFilename, nDipoles, inForwardType,
inOptimizerType, inCriteriaType, inInverterType, inSearchVolumeType, inIntialGuessType)
uif2_rotatingdipolfit(inReferenceDataFileName, inHeadGridFileName,
inSensorConfigurationFileName, outResultFilename, nDipoles, inForwardType,
inOptimizerType, inCriteriaType, inInverterType, inSearchVolumeType, inIntialGuessType)
uif2_fixeddipolfit(inReferenceDataFileName, inHeadGridFileName,
inSensorConfigurationFileName, outResultFilename, nDipoles, inForwardType,
inOptimizerType, inCriteriaType, inInverterType, inSearchVolumeType, inIntialGuessType);

Additional methods for file I/O

uif2_read_ReferenceData(const string inReferenceDataFileName, utMatrix_t<double>
inReferenceData)
uif2_read_SensorConfiguration(const string inSensorConfigurationFileName,
SensorConfiguration inSensorConfiguration, sensortype_e inSensorType)
uif2_write_ResultData(const string outResultFilename, utMatrix_t<double> outResult)

Parameters I

Parameter Type Description File Format
inReferenceDataFileName string Filename of file containing the reference dataVista
inCortexGridFileName string Filename of file containing the description of the cortex gridVista
inBrainSurfaceGridFileName string Filename of file containing the description of the brain surface gridVista
inBrainVolumeGridFileName string Filename of file containing the description of the brain volume gridVista
inHeadGridFileName string Filename of file containing the description of the head grid (needed for simulator)Vista
inSensorConfigurationFileName string Filename of file containing the reference dataVista
outResultFilename string Filename of file containing the resultsVista

Parameters II (switches)

Parameter Possible Values Default
inForwardType forwardtype_Sphere

forwardtype_BEM

forwardtype_FEM

forwardtype_BEM
inInverseType linearinversetype_L2

linearinversetype_Loreta

linearinversetype_ContinuousL2

linearinversetype_ContinuousL2-Gradient

linearinversetype_L2
inNonLinearInverse-Typenonlinearinversetype_L1 nonlinearinversetype_L1
inInverterType invertertype_Tikhonow,

invertertype_TruncatedSVD

invertertype_TruncatedSVD
inOptimizerType optimizertype_SimplexOptimizer

optimizertype_MarquardtOptimizer

optimizertype_SimulatedAnnealing

optimizertype_Marquardt Optimizer
inCriteriaType criteriatype_MinimumSquareError

criteriatype_MaximumEntropy

criteriatype_MaximumProbability

criteriatype_MinimumSquare Error
inSearchVolumeType searchvolumetype_InEntireBrain searchvolumetype_InEntireBrain
inIntialGuessType intialguesstype_Standard intialguesstype_Standard

List of command arguments of user interface III

Inverse Methods:

Linear Estimation
uif3_linear_estimation_oncortex_ with_leadfield inReferenceDataFileName
inCortexGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType inInverseType inInverterType
uif3_linear_estimation_oncortex inReferenceDataFileName inCortexGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename inForwardType
inInverseType inInverterType
uif3_linear_estimation_onbrainsurface _with_leadfield inReferenceDataFileName
inBrainSurfaceGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType inInverseType inInverterType
uif3_linear_estimation_onbrainsurface inReferenceDataFileName inBrainSurfaceGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename inForwardType
inInverseType inInverterType
uif3_linear_estimation_inbrainvolume _with_leadfield inReferenceDataFileName
inBrainVolumeGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType inInverseType inInverterType
uif3_linear_estimation_inbrainvolume inReferenceDataFileName inBrainVolumeGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename inForwardType
inInverseType inInverterType
Non-Linear Estimation
uif3_non_linear_estimation_oncortex_with_leadfield inReferenceDataFileName
inCortexGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType inNonLinearInverseType
inInverterType
uif3_non_linear_estimation_oncortex inReferenceDataFileName inCortexGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename inForwardType
inNonLinearInverseType inInverterType
uif3_non_linear_estimation_onbrainsurface_with_leadfield inReferenceDataFileName
inBrainSurfaceGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType inNonLinearInverseType
inInverterType
uif3_non_linear_estimation_onbrainsurface inReferenceDataFileName
inBrainSurfaceGridFileName inHeadGridFileName inSensorConfigurationFileName
outResultFilename inForwardType inNonLinearInverseType inInverterType
uif3_non_linear_estimation_inbrainvolume_with_leadfield inReferenceDataFileName
inBrainVolumeGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType inNonLinearInverseType
inInverterType
uif3_non_linear_estimation_onbrainsurface inReferenceDataFileName
inBrainSurfaceGridFileName inHeadGridFileName inSensorConfigurationFileName
outResultFilename inForwardType inNonLinearInverseType inInverterType
Goal Function Scan
uif3_goalfunctionscan_oncortex _with_leadfield inReferenceDataFileName
inCortexGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType
uif3_goalfunctionscan_oncortex inReferenceDataFileName inCortexGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename inForwardType
uif3_goalfunctionscan_onbrainsurface _with_leadfield inReferenceDataFileName
inBrainSurfaceGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType
uif3_goalfunctionscan_onbrainsurface inReferenceDataFileName inBrainSurfaceGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename inForwardType
uif3_goalfunctionscan_inbrainvolume _with_leadfield inReferenceDataFileName
inBrainVolumeGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType
uif3_goalfunctionscan_inbrainvolume inReferenceDataFileName inBrainVolumeGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename inForwardType
Music
uif3_MUSIC_oncortex_with_leadfield inReferenceDataFileName inCortexGridFileName
inHeadGridFileName inSensorConfigurationFileName inLeadFieldFileName outResultFilename
inForwardType
uif3_MUSIC_oncortex inReferenceDataFileName inCortexGridFileName inHeadGridFileName
inSensorConfigurationFileName outResultFilename inForwardType
uif3_MUSIC_onbrainsurface_with_leadfield inReferenceDataFileName
inBrainSurfaceGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType
uif3_MUSIC_onbrainsurface inReferenceDataFileName inBrainSurfaceGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename inForwardType
uif3_MUSIC_inbrainvolume_with_leadfield inReferenceDataFileName
inBrainVolumeGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename inForwardType
uif3_MUSIC_inbrainvolume inReferenceDataFileName inBrainVolumeGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename inForwardType
Discrete Dipole Fit
uif3_discrete_dipole_fit_oncortex_with_leadfield inReferenceDataFileName
inCortexGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename nDipoles inForwardType
uif3_discrete_dipole_fit_oncortex inReferenceDataFileName inCortexGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename nDipoles
inForwardType
uif3_discrete_dipole_fit _onbrainsurface_with_leadfield inReferenceDataFileName
inBrainSurfaceGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename nDipoles inForwardType
uif3_discrete_dipole_fit _onbrainsurface inReferenceDataFileName
inBrainSurfaceGridFileName inHeadGridFileName inSensorConfigurationFileName
outResultFilename nDipoles inForwardType
uif3_discrete_dipole_fit_inbrainvolume_with_leadfield inReferenceDataFileName
inBrainVolumeGridFileName inHeadGridFileName inSensorConfigurationFileName
inLeadFieldFileName outResultFilename nDipoles inForwardType
uif3_discrete_dipole_fit_inbrainvolume inReferenceDataFileName inBrainVolumeGridFileName
inHeadGridFileName inSensorConfigurationFileName outResultFilename nDipoles
inForwardType
Dipole Fit
uif3_movingdipolfit inReferenceDataFileName inHeadGridFileName
inSensorConfigurationFileName outResultFilename nDipoles inForwardType inOptimizerType
inCriteriaType inInverterType inSearchVolumeType inIntialGuessType
uif3_rotatingdipolfit inReferenceDataFileName inHeadGridFileName
inSensorConfigurationFileName outResultFilename nDipoles inForwardType inOptimizerType
inCriteriaType inInverterType inSearchVolumeType inIntialGuessType
uif3_fixeddipolfit inReferenceDataFileName inHeadGridFileName
inSensorConfigurationFileName outResultFilename nDipoles inForwardType inOptimizerType
inCriteriaType inInverterType inSearchVolumeType inIntialGuessType

Values for arguments used as switches

Parameter Possible Values Default
inForwardType

Sphere

BEM

FEM

BEM
inInverseType L2

Loreta

ContinuousL2

ContinuousL2Gradient

L2
inNonLinearInverseType L1 L1
inInverterType Tikhonow

TruncatedSVD

TruncatedSVD
inOptimizerType Simplex

Marquardt

SimulatedAnnealing

Marquardt
inCriteriaType MinimumSquareError

MaximumEntropy

MaximumProbability

MinimumSquareError
inSearchVolumeType InEntireBrain

InInfluenceNodes

InEntireBrain
inIntialGuessType Standard Standard
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