SIMBIO/Designreport/Appendix A
From SimBio - A generic environment for bio-numerical simulations
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-Type | nonlinearinversetype_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 data | Vista |
inCortexGridFileName | string | Filename of file containing the description of the cortex grid | Vista |
inBrainSurfaceGridFileName | string | Filename of file containing the description of the brain surface grid | Vista |
inBrainVolumeGridFileName | string | Filename of file containing the description of the brain volume grid | Vista |
inHeadGridFileName | string | Filename of file containing the description of the head grid (needed for simulator) | Vista |
inSensorConfigurationFileName | string | Filename of file containing the reference data | Vista |
outResultFilename | string | Filename of file containing the results | Vista |
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-Type | nonlinearinversetype_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 |